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- PDB-4lxh: Crystal Structure of the S105A mutant of a carbon-carbon bond hyd... -

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Basic information

Entry
Database: PDB / ID: 4lxh
TitleCrystal Structure of the S105A mutant of a carbon-carbon bond hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with 3-Cl HOPDA
ComponentsMCP Hydrolase
KeywordsHYDROLASE / carbon-carbon bond hydrolase / Rossmann Fold / alpha/beta hydrolase fold / cytosolic
Function / homology
Function and homology information


Alpha/beta hydrolase family / 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-C1E / Alpha/beta hydrolase fold
Similarity search - Component
Biological speciesSphingomonas wittichii RW1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsBhowmik, S. / Bolin, J.T.
CitationJournal: Biochemistry / Year: 2013
Title: The Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites.
Authors: Ruzzini, A.C. / Bhowmik, S. / Yam, K.C. / Ghosh, S. / Bolin, J.T. / Eltis, L.D.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: MCP Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4843
Polymers30,2091
Non-polymers2762
Water1,56787
1
A: MCP Hydrolase
hetero molecules

A: MCP Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9686
Polymers60,4172
Non-polymers5514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)66.596, 66.596, 338.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein MCP Hydrolase / Alpha/beta hydrolase fold


Mass: 30208.531 Da / Num. of mol.: 1 / Mutation: S105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas wittichii RW1 (bacteria) / Strain: RW1 / Gene: dxnB2, Swit_3055 / Production host: Escherichia coli (E. coli)
References: UniProt: A5VAT9, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical ChemComp-C1E / (2Z,4E)-3-chloro-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid


Mass: 252.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: grid of sodium malonate (1.5-2.4 M), pH 6.5/7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 6.5-7.0

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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: Apr 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→57.64 Å / Num. all: 30472 / Num. obs: 30456 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.02 Å / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→57.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.645 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25864 1515 5.1 %RANDOM
Rwork0.21454 ---
obs0.21677 28184 97.48 %-
all-30472 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.414 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20.74 Å20 Å2
2--1.47 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.02→57.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 18 87 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222184
X-RAY DIFFRACTIONr_bond_other_d0.0020.021441
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9582963
X-RAY DIFFRACTIONr_angle_other_deg1.00433512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0245277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51323.89595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65315345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.71511
X-RAY DIFFRACTIONr_chiral_restr0.120.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212475
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02452
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.14431370
X-RAY DIFFRACTIONr_mcbond_other0.9563564
X-RAY DIFFRACTIONr_mcangle_it4.64152195
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0848814
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.78411767
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.021→2.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 84 -
Rwork0.321 1754 -
obs--84.12 %

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