1K47 | pdb_00001k47

Crystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK)

PDB DOI: https://doi.org/10.2210/pdb1K47/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae R6
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2001-10-05 Released: 2002-05-08
Deposition Author(s): Romanowski, M.J., Bonanno, J.B., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.215 (Depositor), 0.218 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1K47

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily.

Romanowski, M.J., Bonanno, J.B., Burley, S.K.

(2002) Proteins 47: 568-571

PubMed: 12001237 Search on PubMed
DOI: https://doi.org/10.1002/prot.10118
Primary Citation Related Structures:
1K47

Organizational Affiliation

Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York, USA.

Macromolecule Content

Total Structure Weight: 226.24 kDa
Atom Count: 15,779
Modeled Residue Count: 1,932
Deposited Residue Count: 2,022
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphomevalonate kinase	A, B, C, D, E A, B, C, D, E, F	337	Streptococcus pneumoniae R6	Mutation(s): 7 Gene Names: mvaK2 EC: 2.7.4.2
UniProt
Find proteins for Q8DR49 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DR49 Go to UniProtKB: Q8DR49
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DR49
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, 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: 2.42 Å
R-Value Free: 0.257 (Depositor), 0.260 (DCC)
R-Value Work: 0.215 (Depositor), 0.218 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.606	α = 90
b = 231.606	β = 90
c = 88.587	γ = 120

Software Package:

Software Name	Purpose
SnB	phasing
MLPHARE	phasing
DM	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-05-08

Deposition Author(s):

Romanowski, M.J.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2002-05-08
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Refinement description, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, 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.