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- PDB-2ri6: Crystal Structure of S112A mutant of a C-C hydrolase, BphD from B... -

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Basic information

Entry
Database: PDB / ID: 2ri6
TitleCrystal Structure of S112A 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 / Aromatic hydrocarbons catabolism
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 / :
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
MALONATE ION / 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.68 Å
AuthorsBhowmik, S. / Bolin, J.T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad.
Authors: Horsman, G.P. / Bhowmik, S. / Seah, S.Y. / Kumar, P. / Bolin, J.T. / Eltis, L.D.
History
DepositionOct 10, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 6, 2007ID: 2PU6
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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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)31,9764
Polymers31,7491
Non-polymers2273
Water2,594144
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)127,90516
Polymers126,9974
Non-polymers90812
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 area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.293, 117.293, 87.306
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


Mass: 31749.268 Da / Num. of mol.: 1 / Mutation: S112A / Source method: isolated from a natural source / Source: (natural) Burkholderia xenovorans (bacteria) / Strain: LB400 / References: UniProt: P47229, EC: 3.7.1.-
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.9 M sodium malonate, 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: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 34855 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Rsym value: 12.6 / Net I/σ(I): 18.6
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 8.1 / Num. unique all: 3424 / Rsym value: 27.1 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.68→44.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.825 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1752 5 %RANDOM
Rwork0.175 ---
obs0.176 34845 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: LAST / Resolution: 1.68→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 15 144 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222345
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9553182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76723.964111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1941514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021819
X-RAY DIFFRACTIONr_nbd_refined0.20.21143
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.216
X-RAY DIFFRACTIONr_mcbond_it3.91921420
X-RAY DIFFRACTIONr_mcangle_it5.71532275
X-RAY DIFFRACTIONr_scbond_it9.1532968
X-RAY DIFFRACTIONr_scangle_it11.4283900
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 120 -
Rwork0.202 2385 -
all-2505 -
obs--98.82 %

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