2OP5 | pdb_00002op5

CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (JCVI_PEP_1096672785533) FROM UNCULTURED MARINE ORGANISM AT 2.20 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2OP5/pdb

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

Deposited: 2007-01-26 Released: 2007-02-06
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.292 (Depositor), 0.300 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)
R-Value Observed:
0.233 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hypothetical protein (JCVI_PEP_1096672785533) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 84.18 kDa
Atom Count: 5,563
Modeled Residue Count: 659
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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	117	uncultured marine organism	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth D] G [auth A], H [auth A], I [auth A], J [auth A], K [auth D], L [auth D], M [auth E], N [auth E], O [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.292 (Depositor), 0.300 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)
R-Value Observed: 0.233 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32OP5

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.558	α = 90
b = 84.629	β = 90
c = 144.952	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-02-06
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: 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: 2024-10-09
Changes: Structure summary