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- PDB-5swn: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -

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Basic information

Entry
Database: PDB / ID: 5swn
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Fluoroacetate - Cocrystallized
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / Homodimer / Dehalogenase
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
fluoroacetic acid / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.541 Å
AuthorsMehrabi, P. / Kim, T.H. / Prosser, S.R. / Pai, E.F.
CitationJournal: Science / Year: 2017
Title: The role of dimer asymmetry and protomer dynamics in enzyme catalysis.
Authors: Kim, T.H. / Mehrabi, P. / Ren, Z. / Sljoka, A. / Ing, C. / Bezginov, A. / Ye, L. / Pomes, R. / Prosser, R.S. / Pai, E.F.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)66,5925
Polymers66,4442
Non-polymers1493
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-39 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.880, 78.870, 84.900
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 33221.754 Da / Num. of mol.: 2 / Mutation: D110N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3FO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5 and 200 mM CaCl2 and 19-22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→40.8 Å / Num. obs: 78560 / % possible obs: 99.1 % / Redundancy: 4.6 % / Rsym value: 0.034 / Net I/σ(I): 30.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r3u

3r3u


Resolution: 1.541→40.777 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1935 3896 4.96 %
Rwork0.1691 --
obs0.1703 78560 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.541→40.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4683 0 7 530 5220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074845
X-RAY DIFFRACTIONf_angle_d0.9616595
X-RAY DIFFRACTIONf_dihedral_angle_d22.8972840
X-RAY DIFFRACTIONf_chiral_restr0.055678
X-RAY DIFFRACTIONf_plane_restr0.006863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.541-1.55980.3451060.29852347X-RAY DIFFRACTION87
1.5598-1.57950.30571340.27852493X-RAY DIFFRACTION96
1.5795-1.60030.28071440.21322716X-RAY DIFFRACTION100
1.6003-1.62220.24391580.20312652X-RAY DIFFRACTION100
1.6222-1.64540.23071470.19542647X-RAY DIFFRACTION100
1.6454-1.66990.24241360.18972695X-RAY DIFFRACTION100
1.6699-1.6960.21821430.1922664X-RAY DIFFRACTION100
1.696-1.72390.25441350.17942704X-RAY DIFFRACTION100
1.7239-1.75360.20471430.18332684X-RAY DIFFRACTION100
1.7536-1.78550.24041420.17822645X-RAY DIFFRACTION100
1.7855-1.81980.19451390.18162728X-RAY DIFFRACTION100
1.8198-1.8570.22321400.17762641X-RAY DIFFRACTION100
1.857-1.89730.23951330.1792722X-RAY DIFFRACTION100
1.8973-1.94150.21081480.17782657X-RAY DIFFRACTION100
1.9415-1.990.20891330.17162706X-RAY DIFFRACTION100
1.99-2.04380.18341370.17162643X-RAY DIFFRACTION100
2.0438-2.1040.21041470.17482709X-RAY DIFFRACTION100
2.104-2.17190.18521460.16872671X-RAY DIFFRACTION100
2.1719-2.24950.1821400.16152690X-RAY DIFFRACTION100
2.2495-2.33950.20171310.16722712X-RAY DIFFRACTION100
2.3395-2.4460.17691460.1622686X-RAY DIFFRACTION100
2.446-2.57490.19351460.16442664X-RAY DIFFRACTION100
2.5749-2.73620.21471330.17182700X-RAY DIFFRACTION100
2.7362-2.94740.19261410.17572708X-RAY DIFFRACTION100
2.9474-3.2440.17021440.16662698X-RAY DIFFRACTION100
3.244-3.71310.17661260.15052730X-RAY DIFFRACTION100
3.7131-4.6770.11831450.12842708X-RAY DIFFRACTION99
4.677-40.79090.16891330.15532644X-RAY DIFFRACTION96

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