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- PDB-1td9: Crystal Structure of a Phosphotransacetylase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1td9
TitleCrystal Structure of a Phosphotransacetylase from Bacillus subtilis
ComponentsPhosphate acetyltransferase
KeywordsTRANSFERASE / structural genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


phosphate acetyltransferase activity / phosphate acetyltransferase / acetyl-CoA biosynthetic process / cytoplasm
Similarity search - Function
Isocitrate/Isopropylmalate dehydrogenase-like / Rossmann fold - #10950 / Phosphate acetyltransferase / Phosphate acetyl/butyryltransferase / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Rossmann fold ...Isocitrate/Isopropylmalate dehydrogenase-like / Rossmann fold - #10950 / Phosphate acetyltransferase / Phosphate acetyl/butyryltransferase / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphate acetyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsXu, Q.S. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2005
Title: Crystal structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate
Authors: Xu, Q.S. / Jancarik, J. / Lou, Y. / Kuznetsova, K. / Yakunin, A.F. / Yokota, H. / Adams, P. / Kim, R. / Kim, S.-H.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate acetyltransferase
B: Phosphate acetyltransferase
C: Phosphate acetyltransferase
D: Phosphate acetyltransferase
E: Phosphate acetyltransferase
F: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,33130
Polymers211,0256
Non-polymers2,30624
Water2,054114
1
A: Phosphate acetyltransferase
B: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,20611
Polymers70,3422
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-132 kcal/mol
Surface area26630 Å2
MethodPISA
2
C: Phosphate acetyltransferase
D: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,20611
Polymers70,3422
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-136 kcal/mol
Surface area26610 Å2
MethodPISA
3
E: Phosphate acetyltransferase
hetero molecules

E: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,11010
Polymers70,3422
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
4
F: Phosphate acetyltransferase
hetero molecules

F: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7266
Polymers70,3422
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)185.207, 185.207, 259.414
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein
Phosphate acetyltransferase / Phosphotransacetylase / Vegetative protein 43 / VEG43


Mass: 35170.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PTA, IPA-88D, BSU37660 / Plasmid: pLIC.B4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pSJS1244 / References: UniProt: P39646, phosphate acetyltransferase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: BisTris Propane, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 16, 2003 / Details: mirrors
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. all: 64644 / Num. obs: 64644 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 10.23
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.81 / Num. unique all: 3130 / Rsym value: 0.66 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R5J

1r5j


Resolution: 2.75→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5146040.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1958 3 %RANDOM
Rwork0.268 ---
all0.269 64636 --
obs0.268 64636 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7013 Å2 / ksol: 0.321252 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1-13.2 Å213.57 Å20 Å2
2--13.2 Å20 Å2
3----26.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14682 0 120 114 14916
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it3.032
X-RAY DIFFRACTIONc_mcangle_it4.894
X-RAY DIFFRACTIONc_scbond_it6.714
X-RAY DIFFRACTIONc_scangle_it9.386
LS refinement shellResolution: 2.75→2.8 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 99 3.2 %
Rwork0.41 3030 -
obs-3129 93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SO4_XPLOR.PARSO4_XPLOR.TOP

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