2OD6 | pdb_00002od6

Crystal structure of a dimeric ferredoxin-like protein (jcvi_pep_1096682647733) from uncultured marine organism at 1.85 A resolution

PDB DOI: https://doi.org/10.2210/pdb2OD6/pdb

Classification: UNKNOWN FUNCTION
Organism(s): uncultured marine organism
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-12-21 Released: 2007-01-23
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.231 (Depositor), 0.234 (DCC)
R-Value Work:
0.197 (Depositor), 0.199 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of hypothetical protein (JCVI_PEP_1096682647733) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 53.68 kDa
Atom Count: 4,057
Modeled Residue Count: 433
Deposited Residue Count: 440
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	110	uncultured marine organism	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OHA Query on OHA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	E [auth A], G [auth B], K [auth C], O [auth D]	10-oxohexadecanoic acid C₁₆ H₃₀ O₃ VBFPQNKLKQDSCH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain O [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	F [auth A] H [auth B] I [auth B] J [auth B] L [auth C] F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth D], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.231 (Depositor), 0.234 (DCC)
R-Value Work: 0.197 (Depositor), 0.199 (DCC)
R-Value Observed: 0.198 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.433	α = 90
b = 92.842	β = 90
c = 144.927	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-01-23

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-01-23
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2024-10-30
Changes: Structure summary