6LFD | pdb_00006lfd

Crystal structure of VMB-1 at pH5.5(Bis-Tris)

PDB DOI: https://doi.org/10.2210/pdb6LFD/pdb

Classification: HYDROLASE
Organism(s): Vibrio alginolyticus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-12-02 Released: 2020-02-26
Deposition Author(s): Cheng, Q., Chen, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.200 (Depositor), 0.209 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of VMB-1 at pH 5.5(Bis-Tris)

Chen, S., Cheng, Q.

To be published.

Macromolecule Content

Total Structure Weight: 103.53 kDa
Atom Count: 7,203
Modeled Residue Count: 877
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VMB-1	A, B, C, D	234	Vibrio alginolyticus	Mutation(s): 0 Gene Names: vmb-1 EC: 3.5.2.6
UniProt
Find proteins for A0A5Q5ADH9 (Vibrio alginolyticus) Explore A0A5Q5ADH9 Go to UniProtKB: A0A5Q5ADH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5Q5ADH9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] K [auth C] E [auth A], F [auth A], G [auth B], H [auth B], K [auth C], L [auth C], M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.200 (Depositor), 0.209 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.11	α = 90
b = 97.11	β = 90
c = 132.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Cheng, Q.

Chen, S.

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release
Version 1.1: 2020-03-18
Changes: Database references, Source and taxonomy, Structure summary
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

6LFD | pdb_00006lfd

Crystal structure of VMB-1 at pH5.5(Bis-Tris)

Literature

Crystal structure of VMB-1 at pH 5.5(Bis-Tris)

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand