1X9J | pdb_00001x9j

Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes

PDB DOI: https://doi.org/10.2210/pdb1X9J/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-08-21 Released: 2005-08-30
Deposition Author(s): Diao, J.S., Sanders, D.A., Hasson, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.284 (Depositor), 0.282 (DCC)
R-Value Work:
0.261 (Depositor), 0.260 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of butyrate kinase 2 reveals both open and closed conformations of the two domains: implications for substrate-induced changes

Diao, J.S., Bhattacharyya, S., Ma, Y.L.D., Sanders, D.A., Hasson, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 338.39 kDa
Atom Count: 23,615
Modeled Residue Count: 2,976
Deposited Residue Count: 3,000
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable butyrate kinase 2	A, B, C, D, E A, B, C, D, E, F, G, H	375	Thermotoga maritima	Mutation(s): 0 Gene Names: buk2 EC: 2.7.2.7
UniProt
Find proteins for Q9X278 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X278 Go to UniProtKB: Q9X278
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X278
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain V [auth G] SDF format, chain U [auth G] SDF format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain V [auth G] MOL2 format, chain U [auth G] MOL2 format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain V [auth G] mmCIF format, chain U [auth G] mmCIF format, chain O [auth D]	N [auth D], O [auth D], U [auth G], V [auth G]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain O [auth D] Focus chain U [auth G] Focus chain V [auth G] Interactions & Density Focus chain N [auth D] Focus chain O [auth D] Focus chain U [auth G] Focus chain V [auth G]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain W [auth H] SDF format, chain R [auth E] SDF format, chain J [auth B] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain W [auth H] MOL2 format, chain R [auth E] MOL2 format, chain J [auth B] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain W [auth H] mmCIF format, chain R [auth E] mmCIF format, chain J [auth B]	J [auth B], Q [auth E], R [auth E], S [auth F], W [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain W [auth H] Interactions & Density Focus chain J [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain W [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain T [auth F] SDF format, chain P [auth D] SDF format, chain L [auth C] SDF format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain T [auth F] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain T [auth F] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth B], L [auth C], P [auth D], T [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain T [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain T [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.284 (Depositor), 0.282 (DCC)
R-Value Work: 0.261 (Depositor), 0.260 (DCC)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.68	α = 90
b = 193.68	β = 90
c = 122.932	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-08-30

Deposition Author(s):

Diao, J.S.

Sanders, D.A.

Hasson, M.S.

Revision History (Full details and data files)

Version 1.0: 2005-08-30
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description