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- PDB-3mf7: Crystal Structure of (R)-oxirane-2-carboxylate inhibited cis-CaaD -

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Basic information

Entry
Database: PDB / ID: 3mf7
TitleCrystal Structure of (R)-oxirane-2-carboxylate inhibited cis-CaaD
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / beta-alpha-beta motif / tautomerase / dehalogenase / cis-3-chloroacrylic acid dehalogenase / Isomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGuo, Y. / Serrano, H. / Ernst, S.R. / Johnson Jr., W.H. / Hackert, M.L. / Whitman, C.P.
CitationJournal: Bioorg.Chem. / Year: 2011
Title: Crystal structures of native and inactivated cis-3-chloroacrylic acid dehalogenase: Implications for the catalytic and inactivation mechanisms.
Authors: Guo, Y. / Serrano, H. / Johnson, W.H. / Ernst, S. / Hackert, M.L. / Whitman, C.P.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cis-3-chloroacrylic acid dehalogenase


Theoretical massNumber of molelcules
Total (without water)16,7331
Polymers16,7331
Non-polymers00
Water2,108117
1
A: Cis-3-chloroacrylic acid dehalogenase

A: Cis-3-chloroacrylic acid dehalogenase

A: Cis-3-chloroacrylic acid dehalogenase


Theoretical massNumber of molelcules
Total (without water)50,1983
Polymers50,1983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
Buried area7110 Å2
ΔGint-42 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.783, 96.783, 96.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-243-

HOH

21A-244-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 16732.590 Da / Num. of mol.: 1 / Fragment: UNP residues 2-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Gene: cis-caaD / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: Q6VPE5, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4.6
Details: three micro liter of 15.6mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 0.125 M CaCl2, 0.07 M sodium acetate buffer, 12.5% isopropanol, hanging drop, ...Details: three micro liter of 15.6mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 0.125 M CaCl2, 0.07 M sodium acetate buffer, 12.5% isopropanol, hanging drop, temperature 298K, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 25, 2005
RadiationMonochromator: BLUE MAX-FLUX OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 19123 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.063 / Χ2: 3.096 / Net I/σ(I): 24
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.62-1.684.40.24117512.11791.2
1.68-1.754.60.20319232.289100
1.75-1.824.70.16619122.5899.9
1.82-1.924.40.13318742.97499.5
1.92-2.044.60.10619353.347100
2.04-2.24.70.08619323.39699.9
2.2-2.424.10.07419043.78199.4
2.42-2.774.80.06419373.459100
2.77-3.494.80.05219623.566100
3.49-504.60.04319933.33699.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MF8

3mf8


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.282 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 935 5.2 %RANDOM
Rwork0.186 ---
obs0.188 17952 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.24 Å2 / Biso mean: 9.866 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 0 117 1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021932
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9311259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67923.8347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53415147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.029157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02720
X-RAY DIFFRACTIONr_nbd_refined0.270.2401
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.222
X-RAY DIFFRACTIONr_mcbond_it0.8641.5596
X-RAY DIFFRACTIONr_mcangle_it1.2822922
X-RAY DIFFRACTIONr_scbond_it2.2813372
X-RAY DIFFRACTIONr_scangle_it3.384.5337
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 65 -
Rwork0.21 1251 -
all-1316 -
obs--100 %

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