3D82 | pdb_00003d82

Crystal structure of a cupin-2 domain containing protein (sfri_3543) from shewanella frigidimarina ncimb 400 at 2.05 A resolution

PDB DOI: https://doi.org/10.2210/pdb3D82/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Shewanella frigidimarina NCIMB 400
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-22 Released: 2008-06-10
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.212 (Depositor), 0.222 (DCC)
R-Value Work:
0.186 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Domain of Unknown Function with a Cupin Fold (YP_752209.1) from SHEWANELLA FRIGIDIMARINA NCIMB 400 at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 61.89 kDa
Atom Count: 4,532
Modeled Residue Count: 508
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2, conserved barrel domain protein	A, B, C, D, E	102	Shewanella frigidimarina NCIMB 400	Mutation(s): 0 Gene Names: YP_752209.1, Sfri_3543
UniProt
Find proteins for Q07X94 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q07X94 Go to UniProtKB: Q07X94
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07X94
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D]	N [auth D], Q [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain Q [auth E] Interactions & Density Focus chain N [auth D] Focus chain Q [auth E]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain O [auth E] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain O [auth E] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain O [auth E]	F [auth A], H [auth B], J [auth C], L [auth D], O [auth E]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain O [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain O [auth E]
UNL Query on UNL Download:Ideal Coordinates CCD File	G [auth A], I [auth B], K [auth C], M [auth D], P [auth E]	Unknown ligand VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain P [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain P [auth E]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.212 (Depositor), 0.222 (DCC)
R-Value Work: 0.186 (Depositor), 0.194 (DCC)
R-Value Observed: 0.187 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.92	α = 90
b = 95.14	β = 90
c = 237.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-06-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-06-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary