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- PDB-3r3x: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp... -

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Basic information

Entry
Database: PDB / ID: 3r3x
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Bromoacetate
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / FAcD / Defluorinase / Alpha/beta Hydrolase
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
bromoacetic acid / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChan, P.W.Y. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Mapping the reaction coordinates of enzymatic defluorination.
Authors: Chan, P.W. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F.
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)68,5029
Polymers68,1452
Non-polymers3567
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-65 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.260, 80.170, 85.540
Angle α, β, γ (deg.)90.00, 103.19, 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 / Mutation: D110N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA1163 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-BXA / bromoacetic acid


Mass: 138.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3BrO2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 40.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-24% PEG3350, 0.1-0.2M CaCl2 and 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→83.33 Å / Num. obs: 49450 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.044 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.95
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.4114131833557192.8
1.85-1.90.3174.92127953443193.2
1.9-1.950.226.73125243362193.6
1.95-2.010.1718.35123383308194.3
2.01-2.080.12910.55119843189194.7
2.08-2.150.112.95118073132195.3
2.15-2.230.09214.06114003014195.8
2.23-2.320.07716.65111772950196.3
2.32-2.430.07117.91107182821196.7
2.43-2.550.06519.62102702708197.1
2.55-2.680.05521.799292612197.3
2.68-2.850.04923.5293912469197.6
2.85-3.040.04226.8587892310198.2
3.04-3.290.03531.9982012159198.2
3.29-3.60.02936.4776662020198.6
3.6-4.020.02839.9668451813198.6
4.02-4.650.02643.4761101614198.7
4.65-5.690.02740.9851511362198.3
5.69-8.050.02938.8539741059198.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.76 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.169 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2498 5.1 %RANDOM
Rwork0.1898 ---
obs0.1921 49450 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49 Å2 / Biso mean: 14.6455 Å2 / Biso min: 2.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.39 Å2
2--0.37 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 11 323 4956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224823
X-RAY DIFFRACTIONr_bond_other_d0.0010.023318
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9436566
X-RAY DIFFRACTIONr_angle_other_deg1.07537994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72322.588228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69815732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591538
X-RAY DIFFRACTIONr_chiral_restr0.1120.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021068
X-RAY DIFFRACTIONr_mcbond_it1.051.52937
X-RAY DIFFRACTIONr_mcbond_other0.3431.51171
X-RAY DIFFRACTIONr_mcangle_it1.70824696
X-RAY DIFFRACTIONr_scbond_it2.73531886
X-RAY DIFFRACTIONr_scangle_it4.1614.51870
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 160 -
Rwork0.417 3390 -
all-3550 -
obs--92.74 %

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