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- PDB-2hrw: Crystal Structure of Phosphonopyruvate Hydrolase -

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Basic information

Entry
Database: PDB / ID: 2hrw
TitleCrystal Structure of Phosphonopyruvate Hydrolase
ComponentsPhosphonopyruvate hydrolase
KeywordsHYDROLASE / Phosphonopyruvate Hydrolase / Phosphorus-carbon bond cleavage / phosphonopyruvate / PEP Mutase/Isocitrate Lyase Superfamily
Function / homology
Function and homology information


phosphonopyruvate hydrolase / phosphonopyruvate hydrolase activity / metal ion binding
Similarity search - Function
Phosphonopyruvate hydrolase / Phosphoenolpyruvate phosphomutase / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Phosphonopyruvate hydrolase
Similarity search - Component
Biological speciesVariovorax sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsChen, C.C.H. / Herzberg, O.
CitationJournal: Biochemistry / Year: 2006
Title: Structure and Kinetics of Phosphonopyruvate Hydrolase from Voriovorax sp. Pal2: New Insight into the Divergence of Catalysis within the PEP Mutase/Isocitrate Lyase Superfamily
Authors: Chen, C.C.H. / Han, Y. / Niu, W. / Kulakova, A.N. / Howard, A. / Quinn, J.P. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phosphonopyruvate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3104
Polymers31,2161
Non-polymers943
Water3,045169
1
A: Phosphonopyruvate hydrolase
hetero molecules

A: Phosphonopyruvate hydrolase
hetero molecules

A: Phosphonopyruvate hydrolase
hetero molecules

A: Phosphonopyruvate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,23816
Polymers124,8634
Non-polymers37612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area18910 Å2
ΔGint-179 kcal/mol
Surface area38430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.880, 79.020, 93.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-472-

CL

DetailsThe functional tetramer is formed by the three mutually perpendicular cyrstallographic 2-fold axes in a 222 arrangement.

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Components

#1: Protein Phosphonopyruvate hydrolase


Mass: 31215.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax sp. (bacteria) / Strain: Pal2 / Gene: pphA / Plasmid: pET3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84G06
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.3M xylose, 100 mM HEPES, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→32.62 Å / Num. all: 13871 / Num. obs: 13871 / % possible obs: 95 % / Rmerge(I) obs: 0.08 / Χ2: 1.004 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.656 / Num. unique all: 1370 / Χ2: 1.288 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→32.62 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 613 3.6 %random
Rwork0.204 ---
all0.21 11957 --
obs0.21 11957 --
Solvent computationBsol: 81.158 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 3 169 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0211.5
X-RAY DIFFRACTIONc_angle_deg1.972
LS refinement shellResolution: 2.2→2.26 Å /
RfactorNum. reflection
Rfree0.427 54
Rwork0.411 -
obs-810
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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