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

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Basic information

Entry
Database: PDB / ID: 4lxi
TitleCrystal Structure of the S105A mutant of a carbon-carbon bond hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with 5,8-diF HOPDA
ComponentsMCP Hydrolase
KeywordsHYDROLASE / carbon-carbon bond hydrolase / Rossmann Fold / alpha/beta hydrolase fold / carbon-carbon bond hydrolysis
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-22J / Alpha/beta hydrolase fold
Similarity search - Component
Biological speciesSphingomonas wittichii RW1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsBhowmik, S. / Bolin, J.T.
CitationJournal: Biochemistry / Year: 2013
Title: A substrate-assisted mechanism of nucleophile activation in a ser-his-asp containing C-C bond hydrolase.
Authors: Ruzzini, A.C. / Bhowmik, S. / Ghosh, S. / Yam, K.C. / Bolin, J.T. / Eltis, L.D.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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)30,4863
Polymers30,2091
Non-polymers2772
Water1,26170
1
A: MCP Hydrolase
hetero molecules

A: MCP Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9716
Polymers60,4172
Non-polymers5544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)66.155, 66.155, 342.180
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 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-22J / (3E,5R)-5-fluoro-6-(2-fluorophenyl)-2,6-dioxohex-3-enoic acid


Mass: 254.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8F2O4
#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.: 70 / 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: 3.53 Å3/Da / Density % sol: 65.22 %
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: 2.166→57.27 Å / Num. all: 24889 / Num. obs: 24875 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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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: 2.17→57.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.653 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. HETATM MOLECULE 22J WAS REFINED WITH LIMITED AND RELAXED GEOMETRIC RESTRAINTS TO PERMIT COMPARISON TO THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. HETATM MOLECULE 22J WAS REFINED WITH LIMITED AND RELAXED GEOMETRIC RESTRAINTS TO PERMIT COMPARISON TO THE REFINED COORDINATES OF RELATED LIGANDS FROM PRIOR STUDIES. FOR EXAMPLES, SEE PUBLICATIONS CITED BY PDB ENTRIES 2PUJ, 2RHT, AND 2RHW.
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1253 5.1 %RANDOM
Rwork0.2039 ---
obs0.2066 24540 98.62 %-
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: 89.42 Å2 / Biso mean: 48.4425 Å2 / Biso min: 21.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.17→57.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 19 70 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222176
X-RAY DIFFRACTIONr_bond_other_d0.0020.021436
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9592948
X-RAY DIFFRACTIONr_angle_other_deg0.8743.0013491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46723.93694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21915344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0221511
X-RAY DIFFRACTIONr_chiral_restr0.080.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_mcbond_it1.92531367
X-RAY DIFFRACTIONr_mcbond_other0.4953563
X-RAY DIFFRACTIONr_mcangle_it3.30552189
X-RAY DIFFRACTIONr_scbond_it5.2068809
X-RAY DIFFRACTIONr_scangle_it7.66111760
LS refinement shellResolution: 2.167→2.223 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 90 -
Rwork0.351 1514 -
all-1604 -
obs-24889 89.76 %

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