2P9M | pdb_00002p9m

Crystal structure of conserved hypothetical protein MJ0922 from Methanocaldococcus jannaschii DSM 2661

PDB DOI: https://doi.org/10.2210/pdb2P9M/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-26 Released: 2007-07-03
Deposition Author(s): Zhao, M., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhu, J., Swindell II, J.T., Chen, L., Fu, Z.-Q., Charz, J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.292 (Depositor), 0.297 (DCC)
R-Value Work:
0.222 (Depositor), 0.239 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of conserved hypothetical protein MJ0922 from Methanocaldococcus jannaschii DSM 2661

Zhao, M., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhu, J., Swindell II, J.T., Chen, L., Fu, Z.-Q., Charz, J., Rose, J.P., Wang, B.-C.

To be published.

Macromolecule Content

Total Structure Weight: 62.91 kDa
Atom Count: 4,070
Modeled Residue Count: 514
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein MJ0922	A, B, C, D	138	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 5 Gene Names: MJ0922
UniProt
Find proteins for Q58332 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58332 Go to UniProtKB: Q58332
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58332
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.59 Å
R-Value Free: 0.292 (Depositor), 0.297 (DCC)
R-Value Work: 0.222 (Depositor), 0.239 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.207	α = 90
b = 94.688	β = 90
c = 102.042	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-07-03

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-07-03
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: 2017-09-13
Changes: Advisory, Refinement description
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2024-10-30
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary