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- PDB-4lyd: Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 f... -

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Basic information

Entry
Database: PDB / ID: 4lyd
TitleCrystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1
ComponentsMCP Hydrolase
KeywordsHYDROLASE / meta-cleavage product hydrolase / C-C bond hydrolase / alpha-beta hydrolase / dibenzo-p-dioxin degradation / dibenzofuran degradation
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Alpha/beta hydrolase fold
Function and homology information
Biological speciesSphingomonas wittichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsGhosh, S. / Bolin, J.T. / Bhowmik, S.
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 31, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MCP Hydrolase


Theoretical massNumber of molelcules
Total (without water)30,2091
Polymers30,2091
Non-polymers00
Water1,11762
1
A: MCP Hydrolase

A: MCP Hydrolase


Theoretical massNumber of molelcules
Total (without water)60,4172
Polymers60,4172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)66.317, 66.317, 331.607
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 (bacteria) / Strain: RW1 / Gene: dxnB2, Swit_3055 / Plasmid: pEMDXN1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: A5VAT9, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.5 M sodium malonate, pH 6.8, 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: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 20422 / % possible obs: 93.5 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.078 / Χ2: 1.206 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.336.90.52711380.955154.3
2.33-2.4280.46717451.001182.7
2.42-2.539.20.37320480.99196.4
2.53-2.6711.10.31921331.009199.9
2.67-2.8312.40.22421221.1341100
2.83-3.0512.80.14921591.2841100
3.05-3.36130.10721651.4231100
3.36-3.8513.10.07222031.385199.9
3.85-4.85130.05922341.273199.6
4.85-5012.20.03924751.189199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.22 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.42 Å
Translation2.5 Å43.42 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→43.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2594 / WRfactor Rwork: 0.2047 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7796 / SU B: 7.053 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2197 / SU Rfree: 0.2021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 1036 5.1 %RANDOM
Rwork0.2123 ---
obs0.2147 20323 94.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.57 Å2 / Biso mean: 47.9948 Å2 / Biso min: 27.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.6 Å20 Å2
2--0.6 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.26→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 0 62 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192102
X-RAY DIFFRACTIONr_bond_other_d0.0010.021984
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9512849
X-RAY DIFFRACTIONr_angle_other_deg0.78134561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96223.80492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6715335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2351511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
X-RAY DIFFRACTIONr_mcbond_it3.1884.5661070
X-RAY DIFFRACTIONr_mcbond_other3.1814.5641069
X-RAY DIFFRACTIONr_mcangle_it4.6646.8391334
LS refinement shellResolution: 2.256→2.315 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 42 -
Rwork0.345 816 -
all-858 -
obs--55.86 %

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