2Q5R | pdb_00002q5r

Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase

PDB DOI: https://doi.org/10.2210/pdb2Q5R/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-06-01 Released: 2007-06-12
Deposition Author(s): McGrath, T.E., Soloveychik, M., Romanov, V., Thambipillai, D., Dharamsi, A., Virag, C., Domagala, M., Pai, E.F., Edwards, A.M., Battaile, K., Chirgadze, N.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.283 (Depositor), 0.272 (DCC)
R-Value Work:
0.215 (Depositor), 0.209 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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This is version 1.6 of the entry. See complete history.

Literature

Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase

McGrath, T.E., Soloveychik, M., Romanov, V., Thambipillai, D., Dharamsi, A., Virag, C., Domagala, M., Pai, E.F., Edwards, A.M., Battaile, K., Chirgadze, N.Y.

To be published.

Macromolecule Content

Total Structure Weight: 144.78 kDa
Atom Count: 10,117
Modeled Residue Count: 1,243
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose-6-phosphate kinase	A, B, C, D	330	Staphylococcus aureus	Mutation(s): 2 Gene Names: lacC EC: 2.7.1.144
UniProt
Find proteins for Q5HE12 (Staphylococcus aureus (strain COL)) Explore Q5HE12 Go to UniProtKB: Q5HE12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HE12
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: 2.30 Å
R-Value Free: 0.283 (Depositor), 0.272 (DCC)
R-Value Work: 0.215 (Depositor), 0.209 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.952	α = 90
b = 96.94	β = 94.42
c = 94.485	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-06-12

Deposition Author(s):

Soloveychik, M.

Thambipillai, D.

Chirgadze, N.Y.

Revision History (Full details and data files)

Version 1.0: 2007-06-12
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: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-10-16
Changes: 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.