2Q30 | pdb_00002q30

Crystal structure of a rmlc-like cupin protein (dde_2303) from desulfovibrio desulfuricans subsp. at 1.94 A resolution

PDB DOI: https://doi.org/10.2210/pdb2Q30/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Oleidesulfovibrio alaskensis G20
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-29 Released: 2007-06-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.212 (Depositor), 0.220 (DCC)
R-Value Work:
0.167 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein (YP_388795.1) from Desulfovibrio desulfuricans G20 at 1.94 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 97.76 kDa
Atom Count: 7,119
Modeled Residue Count: 838
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E A, B, C, D, E, F, G, H	110	Oleidesulfovibrio alaskensis G20	Mutation(s): 4 Gene Names: YP_388795.1, Dde_2303
UniProt
Find proteins for Q30YZ6 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q30YZ6 Go to UniProtKB: Q30YZ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q30YZ6
Sequence Annotations Expand
Reference Sequence

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 L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain P [auth H]	I [auth A] J [auth B] K [auth C] M [auth D] N [auth E] I [auth A], J [auth B], K [auth C], M [auth D], N [auth E], O [auth F], P [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth H]

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: 1.94 Å
R-Value Free: 0.212 (Depositor), 0.220 (DCC)
R-Value Work: 0.167 (Depositor), 0.170 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32Q30

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.14	α = 90
b = 133.95	β = 93.04
c = 74.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
Version 1.6: 2024-11-13
Changes: Data collection, Refinement description, Structure summary