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- PDB-3mf8: Crystal Structure of Native cis-CaaD -

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Basic information

Entry
Database: PDB / ID: 3mf8
TitleCrystal Structure of Native cis-CaaD
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / beta-alpha-beta motif / tautomerase / cis-3-chloroacrylic acid dehaloganase / 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: 2.01 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 Jr., 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: Refinement description / Category: 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: 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

Downloads & links

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Assembly

Deposited unit
A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7412
Polymers16,6451
Non-polymers961
Water1,820101
1
A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2226
Polymers49,9343
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7770 Å2
ΔGint-100 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.987, 58.987, 58.297
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-172-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 16644.525 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.76 Å3/Da / Density % sol: 30.07 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 9
Details: three micro liter of 14 mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 8 M (NH4)2SO4, 0.1 M Bicine buffer (pH 9.0), hanging drop, temperature 298K

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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: Mar 29, 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: 2.01→51.1 Å / Num. obs: 7768 / % possible obs: 99.8 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 51.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.01-2.089.80.09199.2
2.08-2.1710.20.083199.9
2.17-2.2610.20.0761100
2.26-2.3810.50.0721100
2.38-2.5310.70.0661100
2.53-2.7310.90.0621100
2.73-3110.0561100
3-3.4411.10.0471100
3.44-4.3311.30.038199.9
4.33-50110.028199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FLT

2flt


Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 9.277 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23574 356 4.6 %RANDOM
Rwork0.18384 ---
obs0.18625 7398 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 0 5 101 1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021932
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9181261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1723.7548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.815148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.688157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02728
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.2417
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2607
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3920.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9681.5594
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6052921
X-RAY DIFFRACTIONr_scbond_it5.33379
X-RAY DIFFRACTIONr_scangle_it4.5084.5340
X-RAY DIFFRACTIONr_rigid_bond_restr5.9253973
X-RAY DIFFRACTIONr_sphericity_free4.8663106
X-RAY DIFFRACTIONr_sphericity_bonded2.8163912
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 19 -
Rwork0.196 549 -
obs--100 %

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