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- PDB-3r3w: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -

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Basic information

Entry
Database: PDB / ID: 3r3w
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Chloroacetate
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / FAcD / Defluorinase / Alpha/beta Hydrolase
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / 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
chloroacetic acid / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChan, P.W.Y. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Mapping the reaction coordinates of enzymatic defluorination.
Authors: Chan, P.W. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F.
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4579
Polymers68,1452
Non-polymers3127
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-68 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.030, 79.770, 85.180
Angle α, β, γ (deg.)90.00, 103.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 34072.676 Da / Num. of mol.: 2 / Mutation: D110N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA1163 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-R3W / chloroacetic acid


Mass: 94.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3ClO2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-24% PEG3350, 0.1-0.2M CaCl2 and 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→83.05 Å / Num. obs: 71601 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.611 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 20.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.640.4143.07148525213197.5
1.64-1.690.3473.91154655066197.6
1.69-1.740.2844.86162644979199
1.74-1.790.2346.01160414843199.4
1.79-1.850.197.37159114744199.3
1.85-1.910.1449.19156464614199.5
1.91-1.980.10512.3151484384199.6
1.98-2.070.0815.31148484228199.5
2.07-2.160.06318.83146004083199.6
2.16-2.260.05621.73141503897199.3
2.26-2.390.04923.86135743711199.7
2.39-2.530.0427.71129453511199.9
2.53-2.70.03431.95123423330199.7
2.7-2.920.03136.05115133093199.9
2.92-3.20.02343.97106152835199.9
3.2-3.580.01951.3597052584199.6
3.58-4.130.01856.9285742276199.9
4.13-5.060.0186172891935199.8
5.06-7.160.0257.2156331506199.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→18.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.974 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 3605 5 %RANDOM
Rwork0.179 ---
obs0.1812 71600 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.92 Å2 / Biso mean: 14.9272 Å2 / Biso min: 2.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.35 Å2
2--0.22 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 0 11 402 5041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224846
X-RAY DIFFRACTIONr_bond_other_d0.0010.023329
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9436601
X-RAY DIFFRACTIONr_angle_other_deg1.1138021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62322.609230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57115734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0281538
X-RAY DIFFRACTIONr_chiral_restr0.1270.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021074
X-RAY DIFFRACTIONr_mcbond_it1.2591.52948
X-RAY DIFFRACTIONr_mcbond_other0.4471.51175
X-RAY DIFFRACTIONr_mcangle_it1.93824716
X-RAY DIFFRACTIONr_scbond_it2.8831898
X-RAY DIFFRACTIONr_scangle_it4.3434.51885
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 253 -
Rwork0.289 4956 -
all-5209 -
obs--97.62 %

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