2CXH | pdb_00002cxh

Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1

PDB DOI: https://doi.org/10.2210/pdb2CXH/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Aeropyrum pernix K1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-06-29 Released: 2005-12-29
Deposition Author(s): Kawazoe, M., Takemoto, C., Hanawa-Suetsugu, K., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.209 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.203 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2CXH

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1

Kawazoe, M., Takemoto, C., Hanawa-Suetsugu, K., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 23.77 kDa
Atom Count: 1,540
Modeled Residue Count: 180
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable brix-domain ribosomal biogenesis protein	A	217	Aeropyrum pernix K1	Mutation(s): 4 Gene Names: APE1443
UniProt
Find proteins for Q9YC08 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YC08 Go to UniProtKB: Q9YC08
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YC08
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.209 (Depositor), 0.220 (DCC)
R-Value Work: 0.184 (Depositor), 0.203 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.171	α = 90
b = 47.364	β = 90
c = 124.675	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-12-29

Deposition Author(s):

Hanawa-Suetsugu, K.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2005-12-29
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.