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- PDB-3t00: Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobiu... -

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Basic information

Entry
Database: PDB / ID: 3t00
TitleCrystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with vanadate
Componentsphosphonoacetate hydrolase
KeywordsHYDROLASE / alkaline phosphatase superfamily / transition state mimic
Function / homology
Function and homology information


phosphonoacetate hydrolase activity / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function
Domain 2, Phosphonoacetate Hydrolase / Phosphonoacetate hydrolase / Phosphonoacetate hydrolase, insert domain superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich ...Domain 2, Phosphonoacetate Hydrolase / Phosphonoacetate hydrolase / Phosphonoacetate hydrolase, insert domain superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / VANADATE ION / Probable phosphonoacetate hydrolase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAgarwal, V. / Nair, S.K.
CitationJournal: Chem.Biol. / Year: 2011
Title: Structural and mechanistic insights into C-p bond hydrolysis by phosphonoacetate hydrolase.
Authors: Agarwal, V. / Borisova, S.A. / Metcalf, W.W. / van der Donk, W.A. / Nair, S.K.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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: phosphonoacetate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8985
Polymers46,5941
Non-polymers3044
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.123, 111.123, 72.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein phosphonoacetate hydrolase


Mass: 46593.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: phnA, RB0978, SM_b21538 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92UV8, nucleotide diphosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2 M NaCl, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 20, 2010
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 42647 / Num. obs: 41825 / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.053 / Χ2: 1.335 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 12.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0056refinement
PDB_EXTRACT3.1data extraction
MD2data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SZY

3szy


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.57 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 2103 5 %RANDOM
Rwork0.2049 ---
obs0.2067 41726 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 67.47 Å2 / Biso mean: 28.9543 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 8 351 3543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223276
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9714459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73422.966145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77715518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8981528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212531
X-RAY DIFFRACTIONr_mcbond_it0.5961.52071
X-RAY DIFFRACTIONr_mcangle_it1.09923333
X-RAY DIFFRACTIONr_scbond_it1.33531205
X-RAY DIFFRACTIONr_scangle_it2.2974.51125
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 146 -
Rwork0.338 2712 -
all-2858 -
obs--92.7 %

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