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- PDB-3v1m: Crystal Structure of the S112A/H265Q mutant of a C-C hydrolase, B... -

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Basic information

Entry
Database: PDB / ID: 3v1m
TitleCrystal Structure of the S112A/H265Q mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, after exposure to its substrate HOPDA
Components2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
KeywordsHYDROLASE / C-C bond hydrolase / Alpha/beta hydrolase fold / BPHD / ALPHA/BETA HYDROLASE / PCB DEGRADATION / META CLEAVAGE PRODUCT HYDROLASE / MCP HYDROLASE / 2-HYDROXY-6-OXO-6-PHENYL-HEXA-2 / 4-DIENOATE HYDROLASE
Function / homology
Function and homology information


2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / aromatic compound catabolic process
Similarity search - Function
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, BphD / Alpha/beta hydrolase family / Epoxide hydrolase-like / 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
(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE / MALONATE ION / 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsGhosh, S. / Bolin, J.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad.
Authors: Ruzzini, A.C. / Ghosh, S. / Horsman, G.P. / Foster, L.J. / Bolin, J.T. / Eltis, L.D.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3623
Polymers32,0431
Non-polymers3192
Water2,180121
1
A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,44812
Polymers128,1714
Non-polymers1,2778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area11340 Å2
ΔGint-50 kcal/mol
Surface area37740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.085, 117.085, 87.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase / HOPDA hydrolase / 2 / 6-dioxo-6-phenylhexa-3-enoate hydrolase


Mass: 32042.633 Da / Num. of mol.: 1 / Mutation: S112A,H265Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: bphD, Bxeno_C1120, Bxe_C1186 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: P47229, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-HPK / (3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE


Mass: 217.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWATER 379 MAY BE A CATION SUCH AS NA+ BUT THIS WAS NOT TESTED

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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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusing, sitting drop, microseeding / pH: 7
Details: 2.4 M Sodium malonate, pH 7.0, VAPOR DIFFUSING, SITTING DROP, MICROSEEDING, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.92→82.79 Å / Num. obs: 23211 / % possible obs: 99.4 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.075 / Χ2: 1.004 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.92-1.9950.38922280.988197
1.99-2.077.30.35822750.9551100
2.07-2.168.40.27823030.9961100
2.16-2.288.60.21423020.9991100
2.28-2.428.60.1523150.9941100
2.42-2.618.60.11323281.0311100
2.61-2.878.60.08623241.049199.9
2.87-3.288.60.0623331.044199.7
3.28-4.148.60.06323610.953199.5
4.14-508.20.04124421.013198

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.92 Å37.03 Å
Translation1.92 Å37.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→82.79 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.1803 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8357 / SU B: 3.516 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1593 / SU Rfree: 0.1475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 1189 5.1 %RANDOM
Rwork0.1803 ---
obs0.1825 23191 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.01 Å2 / Biso mean: 24.7694 Å2 / Biso min: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 1.92→82.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 23 121 2382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192415
X-RAY DIFFRACTIONr_bond_other_d0.0010.021642
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.953279
X-RAY DIFFRACTIONr_angle_other_deg0.83733979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97723.826115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3841514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212765
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02544
LS refinement shellResolution: 1.922→1.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 78 -
Rwork0.256 1421 -
all-1499 -
obs--95.6 %

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