2OGF

Crystal structure of protein MJ0408 from Methanococcus jannaschii, Pfam DUF372

PDB DOI: https://doi.org/10.2210/pdb2OGF/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-01-05 Released: 2007-01-16
Deposition Author(s): Ramagopal, U.A., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.224 (Depositor), 0.230 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.8 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein MJ0408 from Methanococcus jannaschii

Ramagopal, U.A., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 58.69 kDa
Atom Count: 4,488
Modelled Residue Count: 486
Deposited Residue Count: 488
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 MJ0408	A, B, C, D	122	Methanocaldococcus jannaschii	Mutation(s): 3 Gene Names: MJ0408 EC: 4.1.2.25
UniProt
Find proteins for Q57851 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57851 Go to UniProtKB: Q57851
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57851
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OXG Query on OXG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D]	E [auth A], F [auth A], H [auth B], L [auth D]	8-OXOGUANINE C₅ H₃ N₅ O₂ UBKVUFQGVWHZIR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D]	G [auth B], K [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C]	I [auth C], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain I [auth C] Focus chain J [auth C]

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: 1.89 Å
R-Value Free: 0.224 (Depositor), 0.230 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.693	α = 90
b = 46.27	β = 118.54
c = 79.276	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-01-16

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-01-16
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2023-08-30
Changes: Data collection, Database references, Refinement description
Version 1.7: 2023-11-15
Changes: Data collection
Version 1.8: 2024-11-13
Changes: Structure summary