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- PDB-1saz: Membership in the ASKHA Superfamily: Enzymological Properties and... -

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Basic information

Entry
Database: PDB / ID: 1saz
TitleMembership in the ASKHA Superfamily: Enzymological Properties and Crystal Structure of Butyrate Kinase 2 from Thermotoga maritima
ComponentsProbable butyrate kinase 2
KeywordsTRANSFERASE / ASKHA (ACETATE AND SUGAR KINASES / HSC70 / ACTIN) SUPERFAMILY / BUTYRATE KINASE / ACETATE KINASE / ISOBUTYRATE KINASE / TWO SIMILAR DOMAINS / AMPPCP / BUTYRATE / ISOBUTYRATE / DISULFIDE BOND / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / FORMIC ACID / Probable butyrate kinase 2
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsDiao, J. / Cooper, D.R. / Sanders, D.A. / Hasson, M.S.
Citation
Journal: J.Bacteriol. / Year: 2009
Title: Crystal structure of butyrate kinase 2 from Thermotoga maritima, a member of the ASKHA superfamily of phosphotransferases.
Authors: Diao, J. / 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.
History
DepositionFeb 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Probable butyrate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1877
Polymers43,4751
Non-polymers7126
Water1,13563
1
A: Probable butyrate kinase 2
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)353,49856
Polymers347,8008
Non-polymers5,69848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Unit cell
Length a, b, c (Å)197.685, 197.685, 58.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-467-

HOH

DetailsThe biological assembly is an octamer generated from the monomer in the asymmetric unit by the operations: -X,-Y,Z; -Y,X,Z; Y,-X,Z; -X,Y,-Z; X,-Y,-Z; Y,X,-Z; and -Y,-X,-Z

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Components

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


Mass: 43474.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: BUK2, TM1756 / Plasmid: pET30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 MET- (DE3) / References: UniProt: Q9X278, butyrate kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: n-octyl-beta-D-glucoside, Tris-HCl pH 8.5, NaCl, DTT, glycerol, ADP, MgCl2, isobutyrate, sodium formate, acetate. AMPPCP, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9799, 0.9796, 0.9574
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2002 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.97961
30.95741
ReflectionResolution: 2.5→98 Å / Num. obs: 17673 / % possible obs: 87.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 58 Å2 / Rsym value: 0.122 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.67 / Num. unique all: 1296 / Rsym value: 0.567 / % possible all: 65.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→43.64 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2212443.89 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1770 10.2 %RANDOM
Rwork0.217 ---
obs-17670 85.3 %-
Displacement parametersBiso mean: 46.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 32 75 3065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d22.3
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d0.8
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.434 128 10.9 %
Rwork0.336 1048 -
obs--59.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ACP_XPLOR_PAR.TXTACP_XPLOR_TOP.TXT
X-RAY DIFFRACTION5LIGAND.PARLIGAND.TOP

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