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- PDB-1x9j: Structure of butyrate kinase 2 reveals both open- and citrate-ind... -

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Basic information

Entry
Database: PDB / ID: 1x9j
TitleStructure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes
ComponentsProbable butyrate kinase 2
KeywordsTRANSFERASE / ASKHA (ACETATE AND SUGAR KINASES / HSC70 / ACTIN) SUPERFAMILY / BUTYRATE KINASE / ACETATE KINASE / ISOBUTYRATE KINASE / TWO SIMILAR DOMAINS / BUTYRATE / ISOBUTYRATE / ENZYME MECHANISM
Function / homology
Function and homology information


butyrate kinase / butyrate kinase activity / acetate kinase activity / acetate metabolic process / ATP binding / cytoplasm
Similarity search - Function
Butyrate kinase / Acetate and butyrate kinases family signature 2. / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Probable butyrate kinase 2
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDiao, J.S. / Sanders, D.A. / Hasson, M.S.
Citation
Journal: To be Published
Title: Structure of butyrate kinase 2 reveals both open and closed conformations of the two domains: implications for substrate-induced changes
Authors: Diao, J.S. / Bhattacharyya, S. / Ma, Y.L.D. / Sanders, D.A. / Hasson, M.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization of Butyrate Kinase 2 from Thermotoga Maritima Mediated by Vapour Diffusion of Acetic Acid
Authors: Diao, J.S. / Cooper, D.R. / Sanders, D.A. / Hasson, M.S.
#2: Journal: To be Published
Title: Membership in the Askha Superfamily: Enzymological Properties and Crystal Structure of Butyrate Kinase 2 from Thermotoga Maritima
Authors: Diao, J.S. / Cooper, D.R. / Bhattacharyya, S. / Sanders, D.A. / Hasson, M.S.
History
DepositionAug 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable butyrate kinase 2
B: Probable butyrate kinase 2
C: Probable butyrate kinase 2
D: Probable butyrate kinase 2
E: Probable butyrate kinase 2
F: Probable butyrate kinase 2
G: Probable butyrate kinase 2
H: Probable butyrate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,39423
Polymers336,6678
Non-polymers1,72715
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Probable butyrate kinase 2
H: Probable butyrate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3544
Polymers84,1672
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-57 kcal/mol
Surface area28860 Å2
MethodPISA
3
B: Probable butyrate kinase 2
C: Probable butyrate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4465
Polymers84,1672
Non-polymers2793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-57 kcal/mol
Surface area28820 Å2
MethodPISA
4
F: Probable butyrate kinase 2
G: Probable butyrate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7386
Polymers84,1672
Non-polymers5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-56 kcal/mol
Surface area28760 Å2
MethodPISA
5
D: Probable butyrate kinase 2
E: Probable butyrate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8568
Polymers84,1672
Non-polymers6896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-66 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.680, 193.680, 122.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsTHE BIOLOGICAL UNIT IS IDENTICAL TO THE ASYMMETRIC UNIT, WHICH IS AN OCTAMER.

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Probable butyrate kinase 2 / BK 2 / BUK2 / Branched-chain carboxylic acid kinase 2


Mass: 42083.355 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: buk2 / Plasmid: PET30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q9X278, butyrate kinase

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Non-polymers , 5 types, 62 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: CRYSTALLIZATION CONDITIONS: THE PROTEIN SOLUTION CONTAINS 22.5-25 mg/ml BUK2, 25 mM TRIS-HCl pH 8.5, 400 mM NACl, 5 mM DTT, 10%(w/v) GLYCEROL. THE RESERVOIR SOLUTION IS 1ml of 77 mM ...Details: CRYSTALLIZATION CONDITIONS: THE PROTEIN SOLUTION CONTAINS 22.5-25 mg/ml BUK2, 25 mM TRIS-HCl pH 8.5, 400 mM NACl, 5 mM DTT, 10%(w/v) GLYCEROL. THE RESERVOIR SOLUTION IS 1ml of 77 mM PHOSPHATE-CITRATE AND 55% (w/v) PEG 200, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9793 / Wavelength: 0.9793 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. all: 88518 / Num. obs: 88350 / % possible obs: 97 % / Redundancy: 14.2 % / Biso Wilson estimate: 68.8 Å2 / Rsym value: 0.093 / Net I/σ(I): 11.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 7233 / Rsym value: 0.359 / % possible all: 80.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SAZ

1saz


Resolution: 3→91.48 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3022342.25 / Data cutoff low absF: 0 / Isotropic thermal model: ISOROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 8832 10 %RANDOM
Rwork0.261 ---
all-88518 --
obs-88350 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0944 Å2 / ksol: 0.346204 e/Å3
Displacement parametersBiso mean: 55.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→91.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23460 0 108 47 23615
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.612.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.399 705 9.8 %
Rwork0.373 6453 -
obs-6452 79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL_XPLOR_PAR.TXTGOL_XPLOR_TOP.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CIT_PAR.TXTCIT_TOP.TXT

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