3DNM

Crystal Structure Hormone-Sensitive Lipase from a Metagenome Library

PDB DOI: https://doi.org/10.2210/pdb3DNM/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-02 Released: 2009-01-13
Deposition Author(s): Hwang, K.Y., Nam, K.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.282 (Depositor)
R-Value Work:
0.233 (Depositor), 0.230 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural and functional analysis of a novel hormone-sensitive lipase from a metagenome library

Nam, K.H., Kim, M.-Y., Kim, S.-J., Priyadarshi, A., Kwon, S.-T., Koo, B.-S., Yoon, S.-H., Hwang, K.Y.

(2008) Proteins 74: 1036-1040

PubMed: 19089974 Search on PubMed
DOI: https://doi.org/10.1002/prot.22313
Primary Citation of Related Structures:
3DNM

Organizational Affiliation

Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea.

Macromolecule Content

Total Structure Weight: 145.69 kDa
Atom Count: 9,129
Modelled Residue Count: 1,175
Deposited Residue Count: 1,344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase/lipase	A, B, C, D	336	uncultured bacterium	Mutation(s): 0 Gene Names: estE7 EC: 3.1.1
UniProt
Find proteins for Q0GMU1 (uncultured bacterium) Explore Q0GMU1 Go to UniProtKB: Q0GMU1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0GMU1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	E [auth A], H [auth B], P [auth C], S [auth D]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.282 (Depositor)
R-Value Work: 0.233 (Depositor), 0.230 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.321	α = 90
b = 126.828	β = 90
c = 233.393	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Hwang, K.Y.

Nam, K.H.

Revision History (Full details and data files)

Version 1.0: 2009-01-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description