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- PDB-5k3f: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - His... -

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Basic information

Entry
Database: PDB / ID: 5k3f
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - His280Asn/Fluoroacetate - Cocrystallized - Single Protomer Reacted with Ligand
Components(Fluoroacetate dehalogenase) x 2
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: 1.54 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,1933
Polymers68,1572
Non-polymers351
Water12,881715
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-28 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.830, 79.620, 85.230
Angle α, β, γ (deg.)90.000, 103.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 34107.652 Da / Num. of mol.: 1
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: Protein Fluoroacetate dehalogenase


Mass: 34049.617 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
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-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→36.807 Å / Num. obs: 74512 / % possible obs: 92.7 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 19.9
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: 1.54→36.807 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1
RfactorNum. reflection% reflection
Rfree0.2216 3749 5.03 %
Rwork0.1793 --
obs0.1814 74512 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.46 Å2 / Biso mean: 15.7044 Å2 / Biso min: 4.38 Å2
Refinement stepCycle: final / Resolution: 1.54→36.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 1 715 5353
Biso mean--23.15 24.09 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074861
X-RAY DIFFRACTIONf_angle_d1.1546631
X-RAY DIFFRACTIONf_chiral_restr0.044678
X-RAY DIFFRACTIONf_plane_restr0.006874
X-RAY DIFFRACTIONf_dihedral_angle_d13.1081744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5399-1.55940.31441450.27072520266590
1.5594-1.57990.33861390.2582516265590
1.5799-1.60160.31741360.25072531266789
1.6016-1.62450.2731320.23012570270291
1.6245-1.64870.26991520.21852580273292
1.6487-1.67450.23891390.21762573271290
1.6745-1.70190.25321320.19832573270593
1.7019-1.73130.24291430.19472627277092
1.7313-1.76270.25761190.19082617273692
1.7627-1.79660.23811250.19142628275393
1.7966-1.83330.22631260.18962678280493
1.8333-1.87320.24191450.19712606275194
1.8732-1.91680.2861620.2252615277793
1.9168-1.96470.23141360.22652590272693
1.9647-2.01780.24061410.18492692283395
2.0178-2.07720.22991300.20432657278794
2.0772-2.14420.24871520.18762712286496
2.1442-2.22080.21571470.17512677282495
2.2208-2.30970.23591410.19762661280294
2.3097-2.41480.24091470.17262730287797
2.4148-2.54210.22441260.17222764289097
2.5421-2.70140.21731490.1722758290797
2.7014-2.90990.21351430.17232773291698
2.9099-3.20250.21261620.16472793295598
3.2025-3.66560.1841290.15092109223880
3.6656-4.61680.14771240.12172314243887
4.6168-36.81730.16071270.14762899302699

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