4GZV | pdb_00004gzv

Crystal structure of a lipocalin family protein (BACOVA_00364) from Bacteroides ovatus ATCC 8483 at 1.95 A resolution

PDB DOI: https://doi.org/10.2210/pdb4GZV/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacteroides ovatus ATCC 8483
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-06 Released: 2012-11-07
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.220 (Depositor), 0.225 (DCC)
R-Value Work:
0.189 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of a hypothetical protein (BACOVA_00364) from Bacteroides ovatus ATCC 8483 at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 132.75 kDa
Atom Count: 9,393
Modeled Residue Count: 1,084
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B, C, D, E A, B, C, D, E, F, G, H	142	Bacteroides ovatus ATCC 8483	Mutation(s): 0 Gene Names: BACOVA_00364, ZP_02063416.1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain O [auth E] SDF format, chain L [auth C] SDF format, chain K [auth B] MOL2 format, chain S [auth H] MOL2 format, chain O [auth E] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] mmCIF format, chain S [auth H] mmCIF format, chain O [auth E] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B]	K [auth B], L [auth C], O [auth E], S [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth C] Focus chain O [auth E] Focus chain S [auth H] Interactions & Density Focus chain K [auth B] Focus chain L [auth C] Focus chain O [auth E] Focus chain S [auth H]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain Q [auth F]	Q [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth F] Interactions & Density Focus chain Q [auth F]
UNL Query on UNL Download:Ideal Coordinates CCD File	I [auth A], M [auth D], N [auth E], P [auth F], R [auth G]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G] Interactions & Density Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.220 (Depositor), 0.225 (DCC)
R-Value Work: 0.189 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.781	α = 88.23
b = 66.323	β = 82.26
c = 109.737	γ = 74.75

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2012-11-14
Changes: Non-polymer description
Version 1.2: 2013-02-13
Changes: Other
Version 1.3: 2014-12-24
Changes: Structure summary
Version 1.4: 2017-11-15
Changes: Refinement description
Version 1.5: 2018-01-24
Changes: Database references
Version 1.6: 2023-02-01
Changes: Database references, Derived calculations
Version 1.7: 2024-11-06
Changes: Data collection, Refinement description, Structure summary