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- PDB-3v1k: Crystal Structure of the H265Q mutant of a C-C hydrolase, BphD fr... -

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Basic information

Entry
Database: PDB / ID: 3v1k
TitleCrystal Structure of the H265Q mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400.
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 / 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
MALONIC ACID / 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: 2.13 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 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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
B: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2213
Polymers64,1172
Non-polymers1041
Water2,270126
1
A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
B: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)128,4436
Polymers128,2354
Non-polymers2082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area8820 Å2
ΔGint-26 kcal/mol
Surface area37980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.992, 135.992, 65.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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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: 32058.633 Da / Num. of mol.: 2 / Mutation: 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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 2.4 M Sodium malonate, 3 % v/v Ethylene glycol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.125→117.77 Å / Num. obs: 39177 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.122 / Χ2: 1.227 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.12-2.28.20.94838660.9821100
2.2-2.289.20.78938751.1781100
2.28-2.3910.20.60139161.1261100
2.39-2.5110.80.49939211.1761100
2.51-2.67110.34738691.1291100
2.67-2.8811.10.23239191.2061100
2.88-3.1711.20.14839151.3841100
3.17-3.6211.10.09139321.3851100
3.62-4.57110.06639521.3681100
4.57-5010.60.05740121.238199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.44 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.51 Å
Translation2.5 Å44.51 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: 2.13→117.77 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2496 / WRfactor Rwork: 0.2026 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8345 / SU B: 4.842 / SU ML: 0.129 / SU R Cruickshank DPI: 0.2159 / SU Rfree: 0.1873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 1961 5 %RANDOM
Rwork0.1997 ---
obs0.2019 39106 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.15 Å2 / Biso mean: 41.9465 Å2 / Biso min: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.13→117.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 7 126 4623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194628
X-RAY DIFFRACTIONr_bond_other_d0.0010.023166
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9516264
X-RAY DIFFRACTIONr_angle_other_deg0.85237685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90623.973219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77515780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9121528
X-RAY DIFFRACTIONr_chiral_restr0.0680.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
LS refinement shellResolution: 2.125→2.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 139 -
Rwork0.264 2594 -
all-2733 -
obs--99.13 %

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