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- PDB-2puj: Crystal Structure of the S112A/H265A double mutant of a C-C hydro... -

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Basic information

Entry
Database: PDB / ID: 2puj
TitleCrystal Structure of the S112A/H265A double mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with its substrate HOPDA
Components2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
KeywordsHYDROLASE / C-C bond hydrolase / Structural Genomics
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
Chem-HPZ / 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 / Resolution: 1.57 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
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)32,3294
Polymers31,9861
Non-polymers3433
Water2,756153
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)129,31516
Polymers127,9424
Non-polymers1,37312
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 area11500 Å2
ΔGint-68 kcal/mol
Surface area38410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.805, 116.805, 87.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: x, y, z; -x+1/2, -y+1/2, z+1/2; -y, x+1/2, z+1/4; y+1/2, -x, z+3/4;

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Components

#1: Protein 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase


Mass: 31985.582 Da / Num. of mol.: 1 / Mutation: S112A, H265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: bphD / Production host: Escherichia coli (E. coli) / 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.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-HPZ / (2E,4E)-2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOIC ACID


Mass: 218.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.9 M sodium malonate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→82.5 Å / Num. obs: 42069 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rsym value: 8.8 / Net I/σ(I): 21.2
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.5 / Rsym value: 45.8 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OG1

2og1


Resolution: 1.57→82.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.486 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20234 2123 5 %RANDOM
Rwork0.1749 ---
obs0.17627 39930 99.12 %-
all-39930 --
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 mean: 24.286 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.175 Å
Refinement stepCycle: LAST / Resolution: 1.57→82.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 24 153 2411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222343
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.963177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2745294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.524.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54215392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0691514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021829
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21123
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21598
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.51921417
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.10932267
X-RAY DIFFRACTIONr_scbond_it9.42968
X-RAY DIFFRACTIONr_scangle_it12.4833904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 160 -
Rwork0.252 2891 -
obs--98.67 %

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