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- PDB-2ocl: Crystal structure of valacyclovir hydrolase S122A mutant -

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Basic information

Entry
Database: PDB / ID: 2ocl
TitleCrystal structure of valacyclovir hydrolase S122A mutant
ComponentsValacyclovir hydrolase
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


alpha-amino-acid esterase activity / Phase I - Functionalization of compounds / amino acid metabolic process / xenobiotic metabolic process / response to toxic substance / mitochondrial outer membrane / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
Lipases, serine active site. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Valacyclovir hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLai, L. / Xu, Z. / Amidon, G.L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular basis of prodrug activation by human valacyclovirase, an alpha-amino acid ester hydrolase.
Authors: Lai, L. / Xu, Z. / Zhou, J. / Lee, K.D. / Amidon, G.L.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Valacyclovir hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9343
Polymers28,8551
Non-polymers792
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.790, 88.790, 86.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-302-

MG

DetailsThe biological assembly of this molecule is not certain.

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Components

#1: Protein Valacyclovir hydrolase / VACVase / Biphenyl hydrolase-like protein / Biphenyl hydrolase-related protein / Bph-rp / Breast ...VACVase / Biphenyl hydrolase-like protein / Biphenyl hydrolase-related protein / Bph-rp / Breast epithelial mucin-associated antigen / MCNAA


Mass: 28855.080 Da / Num. of mol.: 1 / Mutation: S122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPHL / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q86WA6, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG 4,000, 0.1 M MOPS, 0.1 M MNSO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.39 Å / Num. obs: 30366 / % possible obs: 100 % / Redundancy: 10.81 % / Rmerge(I) obs: 0.083 / Χ2: 0.96 / Net I/σ(I): 15.2 / Scaling rejects: 2481
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.9-1.9710.440.3166.23153630181.15100
1.97-2.0510.590.266.93195730161.04100
2.05-2.1410.610.2148.13220930311.0399.9
2.14-2.2510.640.1719.83222730230.98100
2.25-2.3910.730.14611.43246630180.96100
2.39-2.5810.850.12313.43317830440.92100
2.58-2.8411.060.09816.23353930160.85100
2.84-3.2511.190.08219.33452630570.84100
3.25-4.0911.10.06425.63443730400.88100
4.09-44.3910.830.05432.83453831030.96100

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Processing

Software
NameVersionClassificationNB
d*TREK8.0Ldata processing
CNSrefinement
PDB_EXTRACT2data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.39 Å / σ(F): 0 / Details: Friedel pairs were used in refinement
RfactorNum. reflection% reflection
Rfree0.208 2922 4.9 %
Rwork0.184 --
obs-30366 99.7 %
Solvent computationBsol: 51.866 Å2
Displacement parametersBiso mean: 26.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.277 Å2-0.736 Å20 Å2
2--0.277 Å20 Å2
3----0.554 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 2 285 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1441.5
X-RAY DIFFRACTIONc_scbond_it1.9852
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scangle_it2.8582.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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