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- PDB-5t4t: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -

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Basic information

Entry
Database: PDB / ID: 5t4t
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn - Apo No Halide
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
ACETATE ION / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.511 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 30, 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
B: Fluoroacetate dehalogenase
A: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3826
Polymers68,1452
Non-polymers2364
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-16 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.880, 78.850, 85.130
Angle α, β, γ (deg.)90.00, 103.71, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-H2SO4 pH 8.5, 200 mM calcium acetate and 19-22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.51→82.704 Å / Num. obs: 76737 / % possible obs: 91.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 24.7
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.5 / % possible all: 73.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r3u

3r3u


Resolution: 1.511→82.704 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 3966 5.17 %
Rwork0.1671 --
obs0.169 76737 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.511→82.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 16 659 5372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114894
X-RAY DIFFRACTIONf_angle_d1.1486669
X-RAY DIFFRACTIONf_dihedral_angle_d22.8472858
X-RAY DIFFRACTIONf_chiral_restr0.064682
X-RAY DIFFRACTIONf_plane_restr0.009878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5113-1.52970.2895720.23941559X-RAY DIFFRACTION55
1.5297-1.54910.32461200.25042302X-RAY DIFFRACTION80
1.5491-1.56950.26821360.2342501X-RAY DIFFRACTION89
1.5695-1.5910.26991400.22522521X-RAY DIFFRACTION90
1.591-1.61370.24921280.22382558X-RAY DIFFRACTION89
1.6137-1.63780.31121350.21382580X-RAY DIFFRACTION91
1.6378-1.66340.27081330.20462547X-RAY DIFFRACTION90
1.6634-1.69070.24571230.20482607X-RAY DIFFRACTION91
1.6907-1.71980.25521650.2032570X-RAY DIFFRACTION91
1.7198-1.75110.22861480.1982569X-RAY DIFFRACTION91
1.7511-1.78480.25241490.19362626X-RAY DIFFRACTION93
1.7848-1.82120.23121250.18532597X-RAY DIFFRACTION90
1.8212-1.86080.21371660.1822608X-RAY DIFFRACTION93
1.8608-1.90410.2331300.18162630X-RAY DIFFRACTION92
1.9041-1.95170.20671360.17482625X-RAY DIFFRACTION93
1.9517-2.00450.23091570.17762636X-RAY DIFFRACTION93
2.0045-2.06350.23291570.17132632X-RAY DIFFRACTION94
2.0635-2.13010.20941460.17162688X-RAY DIFFRACTION94
2.1301-2.20620.19181450.16222659X-RAY DIFFRACTION93
2.2062-2.29460.19191650.16382674X-RAY DIFFRACTION95
2.2946-2.3990.19091760.16152673X-RAY DIFFRACTION95
2.399-2.52550.21661320.1592714X-RAY DIFFRACTION95
2.5255-2.68380.20231510.16392723X-RAY DIFFRACTION95
2.6838-2.8910.18881550.16362727X-RAY DIFFRACTION96
2.891-3.18190.1871250.15392771X-RAY DIFFRACTION96
3.1819-3.64240.17141490.14292773X-RAY DIFFRACTION97
3.6424-4.58890.1541320.12352853X-RAY DIFFRACTION98
4.5889-82.82780.14441700.14332848X-RAY DIFFRACTION98

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