6D5C | pdb_00006d5c

Structure of Caldicellulosiruptor danielii GH10 module of glycoside hydrolase WP_045175321

PDB DOI: https://doi.org/10.2210/pdb6D5C/pdb

Classification: HYDROLASE
Organism(s): Anaerocellum danielii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-19 Released: 2019-04-24
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.233 (Depositor), 0.240 (DCC)
R-Value Work:
0.179 (Depositor), 0.187 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species

Conway, J.M., Crosby, J.R., Hren, A.P., Southerland, R.T., Lee, L.L., Lunin, V.V., Alahuhta, P.M., Himmel, M.E., Bomble, Y.J., Adams, M.W.W., Kelly, R.M.

(2019) AIChE J

DOI: https://doi.org/10.1002/aic.16354

Macromolecule Content

Total Structure Weight: 124.72 kDa
Atom Count: 10,027
Modeled Residue Count: 1,011
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycoside hydrolase WP_045175321	A, B, C	350	Anaerocellum danielii	Mutation(s): 0 EC: 3.2.1 (PDB Primary Data), 3.2.1.8 (UniProt)
UniProt
Find proteins for A0A4V8GZQ8 (Anaerocellum danielii) Explore A0A4V8GZQ8 Go to UniProtKB: A0A4V8GZQ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4V8GZQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain FA [auth C] SDF format, chain F [auth A] SDF format, chain EA [auth C] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth C]	CA [auth C] D [auth A] DA [auth C] E [auth A] EA [auth C] CA [auth C], D [auth A], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth C] Focus chain D [auth A] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain D [auth A] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain M [auth A] SDF format, chain Z [auth B] SDF format, chain N [auth A] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain N [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain N [auth A] mmCIF format, chain BA [auth B]	AA [auth B], BA [auth B], M [auth A], N [auth A], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	IA [auth C] J [auth A] K [auth A] L [auth A] W [auth B] IA [auth C], J [auth A], K [auth A], L [auth A], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.233 (Depositor), 0.240 (DCC)
R-Value Work: 0.179 (Depositor), 0.187 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.307	α = 90
b = 98.497	β = 93.58
c = 78.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
PROTEUM PLUS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Alahuhta, P.M.

Lunin, V.V.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2019-06-05
Changes: Data collection, Database references
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description