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- PDB-3r40: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -

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Basic information

Entry
Database: PDB / ID: 3r40
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo
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
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,3638
Polymers68,1452
Non-polymers2176
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-76 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.930, 79.270, 85.080
Angle α, β, γ (deg.)90.000, 103.220, 90.000
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-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å
DetectorDate: Apr 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.05→82.82 Å / Num. obs: 243420 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.665 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.92
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.05-1.080.2663.673822416990191.4
1.08-1.110.2044.674148316894193.7
1.11-1.140.1466.164293916791195.5
1.14-1.170.127.494403516454196.3
1.17-1.210.118.324500316076197.1
1.21-1.250.09410.114562115640197.6
1.25-1.30.08211.724608815149197.8
1.3-1.360.07213.164615114602197.8
1.36-1.420.06415.024597414011198.4
1.42-1.480.05517.664556613430198.4
1.48-1.570.04720.654482912882198.8
1.57-1.660.07523.826486912204199.3
1.66-1.770.07126.777470811525199.8
1.77-1.920.06229.846777610711199.3
1.92-2.10.05431.65575079847199
2.1-2.350.04932.22463078809198.3
2.35-2.710.0429.16322907764198
2.71-3.320.03428.24221946547197.3
3.32-4.70.03129.41152294788191.5

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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: 1.05→41.41 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.757 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.168 12237 5 %RANDOM
Rwork0.1441 ---
obs0.1453 243419 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.92 Å2 / Biso mean: 14.5701 Å2 / Biso min: 4.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.1 Å2
2--0.31 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.05→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 6 397 5002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0214976
X-RAY DIFFRACTIONr_bond_other_d0.0010.023439
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.9416788
X-RAY DIFFRACTIONr_angle_other_deg1.1838297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8522.5236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53615773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.661541
X-RAY DIFFRACTIONr_chiral_restr0.1560.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215679
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021119
X-RAY DIFFRACTIONr_mcbond_it2.6351.53021
X-RAY DIFFRACTIONr_mcbond_other1.0081.51199
X-RAY DIFFRACTIONr_mcangle_it3.64424851
X-RAY DIFFRACTIONr_scbond_it4.8431955
X-RAY DIFFRACTIONr_scangle_it6.7114.51937
X-RAY DIFFRACTIONr_rigid_bond_restr2.22238415
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 865 -
Rwork0.23 16115 -
all-16980 -
obs--91.42 %

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