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- PDB-5k3c: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/... -

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Basic information

Entry
Database: PDB / ID: 5k3c
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/5-Fluorotryptophan
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
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
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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)68,5785
Polymers68,4712
Non-polymers1063
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-50 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.890, 79.460, 85.240
Angle α, β, γ (deg.)90.000, 103.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 34235.574 Da / Num. of mol.: 2
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350 19-22%, 200mM Calcium chloride, 100mM Tris HCL pH 8.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.541→19.138 Å / Num. obs: 77192 / % possible obs: 96.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 25.2
Reflection shellResolution: 1.54→1.58 Å / Rmerge(I) obs: 0.214

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R3U

3r3u


Resolution: 1.541→19.138 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.2113 3883 5.03 %
Rwork0.1736 --
obs0.1756 77192 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.87 Å2 / Biso mean: 16.3898 Å2 / Biso min: 4.47 Å2
Refinement stepCycle: final / Resolution: 1.541→19.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 3 573 5193
Biso mean--16.8 24.21 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134821
X-RAY DIFFRACTIONf_angle_d1.5886581
X-RAY DIFFRACTIONf_chiral_restr0.062668
X-RAY DIFFRACTIONf_plane_restr0.008857
X-RAY DIFFRACTIONf_dihedral_angle_d13.4161747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5412-1.560.2847990.32391813191267
1.56-1.57970.30181370.2682419255690
1.5797-1.60050.24781400.2032586272696
1.6005-1.62240.25171320.19972602273496
1.6224-1.64560.24191310.19912604273596
1.6456-1.67010.24671610.19192616277796
1.6701-1.69620.27911260.19192611273796
1.6962-1.7240.24081340.18552626276097
1.724-1.75370.22421250.18932645277097
1.7537-1.78560.21991400.18362593273397
1.7856-1.81990.22231150.18322706282197
1.8199-1.8570.23261300.18822640277098
1.857-1.89740.231330.18612645277897
1.8974-1.94150.23451270.19242645277297
1.9415-1.990.24451390.19082690282998
1.99-2.04370.22261510.18362608275998
2.0437-2.10380.18881600.18392695285599
2.1038-2.17160.23341560.1762635279199
2.1716-2.24910.2551360.17692663279998
2.2491-2.3390.21911500.18252678282898
2.339-2.44520.22221520.17592682283499
2.4452-2.57390.2251410.16862689283099
2.5739-2.73470.18811430.17122683282699
2.7347-2.94520.22991710.182690286199
2.9452-3.24030.181390.16992725286499
3.2403-3.70620.19141360.16122713284999
3.7062-4.65820.15271410.12412740288199
4.6582-19.13940.17241380.15132667280596

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