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- PDB-4lxg: Crystal structure of DxnB2, a carbon - carbon bond hydrolase from... -

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Basic information

Entry
Database: PDB / ID: 4lxg
TitleCrystal structure of DxnB2, a carbon - carbon bond hydrolase from Sphingomonas wittichii RW1
ComponentsMCP Hydrolase
KeywordsHYDROLASE / Carbon-carbon bond hydrolase / Rossmann Fold / alpha/beta hydrolase fold / Cytosolic
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 RW1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MCP Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5134
Polymers30,2251
Non-polymers2883
Water1,45981
1
A: MCP Hydrolase
hetero molecules

A: MCP Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0258
Polymers60,4492
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)66.983, 66.983, 327.743
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: 30224.531 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2
Details: grid of ammonium sulfate (1.0-2.5 M) containing 0.1 M Tris, pH 8.2 and 6-10% ethanol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→58.03 Å / Num. all: 22668 / Num. obs: 22668 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.2 Å / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J1I

1j1i


Resolution: 2.22→36.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.378 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1150 5.1 %RANDOM
Rwork0.2017 ---
obs0.2033 22550 99.48 %-
all-22668 --
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 max: 119.64 Å2 / Biso mean: 52.9638 Å2 / Biso min: 31.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.75 Å20 Å2
2--0.75 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.22→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 15 81 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192157
X-RAY DIFFRACTIONr_angle_refined_deg1.0171.9592928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.924.02292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50215341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2951510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211641
X-RAY DIFFRACTIONr_mcbond_it2.1295.0261099
X-RAY DIFFRACTIONr_mcangle_it3.1449.3941372
X-RAY DIFFRACTIONr_scbond_it3.4655.4421058
LS refinement shellResolution: 2.223→2.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 71 -
Rwork0.273 1518 -
all-1589 -
obs--98.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.47620.8821-0.30511.8348-1.28812.9718-0.05890.31390.36150.1611-0.06150.0994-0.14740.43720.12040.0420.04080.03290.3830.24660.1813-21.793128.02115.0521
23.95631.99580.30892.0104-0.1983.4438-0.06060.5644-0.3754-0.32260.0053-0.28360.38980.42090.05530.11790.10770.05630.56930.15670.2183-19.176717.4550.432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 137
2X-RAY DIFFRACTION1A204 - 276
3X-RAY DIFFRACTION2A138 - 203

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