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- PDB-1r5j: Crystal Structure of a Phosphotransacetylase from Streptococcus p... -

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Basic information

Entry
Database: PDB / ID: 1r5j
TitleCrystal Structure of a Phosphotransacetylase from Streptococcus pyogenes
Componentsputative phosphotransacetylasePhosphate acetyltransferase
KeywordsTRANSFERASE / lactate dehydrogenase-like nucleotide-binding fold / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


acetyltransferase activity
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative phosphotransacetylase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsXu, Q.S. / Shin, D.H. / Pufan, R. / Yokota, H. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a phosphotransacetylase from Streptococcus pyogenes.
Authors: Xu, Q.S. / Shin, D.H. / Pufan, R. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionOct 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative phosphotransacetylase
B: putative phosphotransacetylase


Theoretical massNumber of molelcules
Total (without water)73,3462
Polymers73,3462
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-22 kcal/mol
Surface area26330 Å2
MethodPISA
2
A: putative phosphotransacetylase
B: putative phosphotransacetylase

A: putative phosphotransacetylase
B: putative phosphotransacetylase


Theoretical massNumber of molelcules
Total (without water)146,6934
Polymers146,6934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_445z-1/4,-y-1/4,x+1/41
Buried area10160 Å2
ΔGint-53 kcal/mol
Surface area48670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.725, 173.725, 173.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein putative phosphotransacetylase / Phosphate acetyltransferase


Mass: 36673.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: pLIC.B4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pSJS1244 / References: UniProt: Q99ZQ5, phosphate acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.05 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 298 K / pH: 5.5
Details: BisTris, PEG 3350, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9797, 0.9794, 0.9500
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2003 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97941
30.951
ReflectionResolution: 2.7→20 Å / Num. obs: 25144 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 23.2 % / Biso Wilson estimate: 69.9 Å2 / Rsym value: 0.119 / Net I/σ(I): 23.9
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3842196.04 / 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
Rfree0.281 2537 10.1 %RANDOM
Rwork0.229 ---
obs0.229 25109 99.9 %-
all-25109 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 72.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 0 30 5034
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.271.5
X-RAY DIFFRACTIONc_mcangle_it7.712
X-RAY DIFFRACTIONc_scbond_it8.482
X-RAY DIFFRACTIONc_scangle_it112.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.418 231 9.4 %
Rwork0.397 2229 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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