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- PDB-8fir: Crystal structure of TpPta, a phosphotransacetylase from Treponem... -

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Basic information

Entry
Database: PDB / ID: 8fir
TitleCrystal structure of TpPta, a phosphotransacetylase from Treponema pallidum
ComponentsPhosphate acetyltransferase
KeywordsTRANSFERASE / phosphotransacetylase / syphilis / T. pallidum / metabolic enzyme
Function / homology
Function and homology information


phosphate acetyltransferase activity / phosphate acetyltransferase
Similarity search - Function
Phosphate acetyltransferase / Phosphate acetyl/butyryltransferase / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase
Similarity search - Domain/homology
CITRIC ACID / phosphate acetyltransferase
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBrautigam, C.A. / Norgard, M.V. / Deka, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Plos One / Year: 2023
Title: Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum.
Authors: Brautigam, C.A. / Deka, R.K. / Tso, S.C. / Liu, W.Z. / Norgard, M.V.
History
DepositionDec 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate acetyltransferase
B: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0494
Polymers77,7952
Non-polymers2542
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Verified by analytical ultracentrifugation in the sedimentation velocity mode and by mass photometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-20 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.195, 66.195, 337.642
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

21A-676-

HOH

31A-687-

HOH

41B-648-

HOH

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Components

#1: Protein Phosphate acetyltransferase


Mass: 38897.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: pta, FA889_00490 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7Z2EMN2, phosphate acetyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate dibasic, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 63299 / % possible obs: 98.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.09 Å2 / Rrim(I) all: 0.094 / Net I/σ(I): 14.6
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 3101 / Rrim(I) all: 0.745

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→36.91 Å / SU ML: 0.2091 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2176 3202 5.06 %
Rwork0.1795 60084 -
obs0.1814 63286 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.33 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 17 337 5424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115180
X-RAY DIFFRACTIONf_angle_d1.07617005
X-RAY DIFFRACTIONf_chiral_restr0.0604818
X-RAY DIFFRACTIONf_plane_restr0.0081922
X-RAY DIFFRACTIONf_dihedral_angle_d21.07471946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.27041280.24272456X-RAY DIFFRACTION95.88
1.98-2.010.3211470.23522605X-RAY DIFFRACTION99.53
2.01-2.040.27721330.22572542X-RAY DIFFRACTION99.7
2.04-2.080.27511230.21762657X-RAY DIFFRACTION99.32
2.08-2.120.26751350.20532571X-RAY DIFFRACTION99.49
2.12-2.160.26531390.20752586X-RAY DIFFRACTION99.42
2.16-2.20.25741650.19642611X-RAY DIFFRACTION99.39
2.2-2.250.21431260.19892593X-RAY DIFFRACTION99.34
2.25-2.30.24331410.19822610X-RAY DIFFRACTION99.35
2.3-2.360.23221470.19262588X-RAY DIFFRACTION99.35
2.36-2.420.26181350.1912592X-RAY DIFFRACTION99.13
2.42-2.490.27011270.19882636X-RAY DIFFRACTION99.1
2.49-2.570.22811320.18742591X-RAY DIFFRACTION99.02
2.57-2.660.21541390.17932649X-RAY DIFFRACTION98.94
2.66-2.770.18271500.18172571X-RAY DIFFRACTION98.41
2.77-2.90.27451290.19192623X-RAY DIFFRACTION98.6
2.9-3.050.23351420.19032612X-RAY DIFFRACTION98.57
3.05-3.240.2161450.18622634X-RAY DIFFRACTION98.48
3.24-3.490.19611480.17972652X-RAY DIFFRACTION98.49
3.49-3.840.21521310.16152648X-RAY DIFFRACTION98.34
3.84-4.40.16781640.14462654X-RAY DIFFRACTION97.81
4.4-5.530.18231360.14142653X-RAY DIFFRACTION96.31
5.54-36.910.20441400.18382750X-RAY DIFFRACTION93.53

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