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- PDB-5k3e: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -

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Basic information

Entry
Database: PDB / ID: 5k3e
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - 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
GLYCOLIC ACID / 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)68,2925
Polymers68,1452
Non-polymers1473
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-37 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.880, 78.990, 84.980
Angle α, β, γ (deg.)90.000, 103.230, 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-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#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.: 648 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
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 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→19.8 Å / Num. obs: 78608 / % possible obs: 99.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 24
Reflection shellResolution: 1.54→1.58 Å / Rmerge(I) obs: 0.17

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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→19.776 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.59
RfactorNum. reflection% reflection
Rfree0.2022 3942 5.01 %
Rwork0.1658 --
obs0.1676 78608 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.89 Å2 / Biso mean: 16.0274 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: final / Resolution: 1.54→19.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 7 648 5308
Biso mean--16.07 24.92 -
Num. residues----589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184856
X-RAY DIFFRACTIONf_angle_d1.7916620
X-RAY DIFFRACTIONf_chiral_restr0.084678
X-RAY DIFFRACTIONf_plane_restr0.011871
X-RAY DIFFRACTIONf_dihedral_angle_d13.7431743
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 (%)
1.54-1.55880.44361100.44872132224279
1.5588-1.57850.30091220.28812407252990
1.5785-1.59930.25311500.202626862836100
1.5993-1.62120.25621460.185827132859100
1.6212-1.64430.21991380.183726552793100
1.6443-1.66890.20921440.180327042848100
1.6689-1.69490.22761430.182726452788100
1.6949-1.72270.24141300.172527032833100
1.7227-1.75240.2521290.180327272856100
1.7524-1.78420.20121280.170926832811100
1.7842-1.81850.24141480.170127182866100
1.8185-1.85560.20241340.160826812815100
1.8556-1.89590.23011390.162227012840100
1.8959-1.940.21271320.163226832815100
1.94-1.98850.23021310.168127392870100
1.9885-2.04220.19081440.164826502794100
2.0422-2.10220.22331420.168227272869100
2.1022-2.170.19371490.163526732822100
2.17-2.24740.21781350.161827102845100
2.2474-2.33730.20771550.168326992854100
2.3373-2.44350.20151590.163326782837100
2.4435-2.57210.20341700.162726642834100
2.5721-2.73280.20511420.167827052847100
2.7328-2.94320.21481490.17827062855100
2.9432-3.23820.20941560.160927032859100
3.2382-3.70410.18181400.151227242864100
3.7041-4.65670.14041380.127527352873100
4.6567-19.77740.1561390.15332715285498

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