2PLR | pdb_00002plr

Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

PDB DOI: https://doi.org/10.2210/pdb2PLR/pdb

Classification: TRANSFERASE
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-20 Released: 2008-04-22
Deposition Author(s): Kanaujia, S.P., Jeyakanthan, J., Rafi, Z.A., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

Kanaujia, S.P., Jeyakanthan, J., Rafi, Z.A., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 52.91 kDa
Atom Count: 4,170
Modeled Residue Count: 420
Deposited Residue Count: 426
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thymidylate kinase	A, B	213	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 EC: 2.7.4.9
UniProt
Find proteins for Q970Q8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970Q8 Go to UniProtKB: Q970Q8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q970Q8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain F [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain F [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	F [auth A], V [auth B], W [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain F [auth A] Focus chain V [auth B] Focus chain W [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]
DTT Query on DTT Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] O [auth A] BA [auth B], CA [auth B], DA [auth B], EA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	J [auth A] K [auth A] L [auth A] X [auth B] Y [auth B] J [auth A], K [auth A], L [auth A], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.523	α = 90
b = 62.873	β = 90
c = 137.332	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-04-22

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-04-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary