4DWJ

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

PDB DOI: https://doi.org/10.2210/pdb4DWJ/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-02-24 Released: 2012-03-07
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.268
R-Value Work: 0.201
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 211.84 kDa
Atom Count: 12,937
Modelled Residue Count: 1,589
Deposited Residue Count: 1,832
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B, C, D, E A, B, C, D, E, F, G, H	229	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: tmk, SAV0482 EC: 2.7.4.9
UniProt
Find proteins for P65248 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P65248 Go to UniProtKB: P65248
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P65248
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TMP Query on TMP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth F] SDF format, chain N [auth G] SDF format, chain O [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth F] MOL2 format, chain N [auth G] MOL2 format, chain O [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth F] I [auth A], J [auth B], K [auth C], L [auth D], M [auth F], N [auth G], O [auth H]	THYMIDINE-5'-PHOSPHATE C₁₀ H₁₅ N₂ O₈ P GYOZYWVXFNDGLU-XLPZGREQSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth G] Focus chain O [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth G] Focus chain O [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.268
R-Value Work: 0.201
R-Value Observed: 0.204
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M34DWJ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.662	α = 81.48
b = 73.409	β = 90.1
c = 96.868	γ = 90.12

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2012-04-11
Changes: Structure summary
Version 1.2: 2012-10-10
Changes: Structure summary
Version 1.3: 2017-11-15
Changes: Refinement description
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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4DWJ

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)