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- PDB-5k3b: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -

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Basic information

Entry
Database: PDB / ID: 5k3b
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Chloroacetate - 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
chloroacetic acid / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 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)68,3115
Polymers68,1452
Non-polymers1653
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-39 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.837, 78.956, 84.986
Angle α, β, γ (deg.)90.000, 103.280, 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 (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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-R3W / chloroacetic acid


Mass: 94.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3ClO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 39.97 %
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: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→18.8 Å / Num. obs: 72586 / % possible obs: 98.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 18.9
Reflection shellResolution: 1.58→1.66 Å / Rmerge(I) obs: 0.252

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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: 1.58→18.792 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.51
RfactorNum. reflection% reflection
Rfree0.1964 3654 5.03 %
Rwork0.1644 --
obs0.1659 72586 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.52 Å2 / Biso mean: 16.6758 Å2 / Biso min: 4.94 Å2
Refinement stepCycle: final / Resolution: 1.58→18.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 7 569 5240
Biso mean--18.51 24.47 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014880
X-RAY DIFFRACTIONf_angle_d1.3146651
X-RAY DIFFRACTIONf_chiral_restr0.054679
X-RAY DIFFRACTIONf_plane_restr0.007875
X-RAY DIFFRACTIONf_dihedral_angle_d13.381755
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.60080.27561380.21762531266994
1.6008-1.62270.27261500.20432593274397
1.6227-1.64590.21531210.2032593271497
1.6459-1.67040.25871440.19792619276397
1.6704-1.69650.26161190.19612604272397
1.6965-1.72430.24311560.18792618277498
1.7243-1.7540.23391360.18762636277298
1.754-1.78590.23211430.18322615275898
1.7859-1.82020.23821280.17982678280699
1.8202-1.85730.22031580.17572577273598
1.8573-1.89770.21781280.17742707283599
1.8977-1.94180.21761560.17092606276299
1.9418-1.99030.22271490.17512665281499
1.9903-2.0440.21221310.17162636276799
2.044-2.10410.21961320.174926962828100
2.1041-2.17190.18311390.16642671281099
2.1719-2.24940.20551430.16792656279999
2.2494-2.33930.21541440.171226892833100
2.3393-2.44560.17951440.159326812825100
2.4456-2.57420.19251360.166526782814100
2.5742-2.73510.1961310.168426912822100
2.7351-2.94550.19131610.177426792840100
2.9455-3.24060.20031590.161226752834100
3.2406-3.70640.19011280.152527172845100
3.7064-4.65780.13831350.123227252860100
4.6578-18.79320.13871450.13952696284198

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