4Z48

Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution

PDB DOI: https://doi.org/10.2210/pdb4Z48/pdb

Classification: Structural Biology, Unknown Function
Organism(s): Desulfovibrio piger ATCC 29098
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-01 Released: 2015-04-22
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.248
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 59.01 kDa
Atom Count: 4,552
Modelled Residue Count: 480
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	246	Desulfovibrio piger ATCC 29098	Mutation(s): 0 Gene Names: DESPIG_00262
UniProt
Find proteins for B6WQE2 (Desulfovibrio piger ATCC 29098) Explore B6WQE2 Go to UniProtKB: B6WQE2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B6WQE2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B]	F [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.248
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M3HC71

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.4	α = 100.71
b = 56.34	β = 97.04
c = 65.56	γ = 109.01

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER	refinement
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2015-04-22
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2023-02-01
Changes: Database references, Derived calculations

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Help and Resources

4Z48

Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution

Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger ATCC 29098 at 1.75 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)