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- PDB-3r3u: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/apo -

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Basic information

Entry
Database: PDB / ID: 3r3u
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/apo
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
NICKEL (II) ION / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
C: Fluoroacetate dehalogenase
D: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,61311
Polymers136,2954
Non-polymers3187
Water18,7181039
1
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3366
Polymers68,1472
Non-polymers1884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-47 kcal/mol
Surface area21980 Å2
MethodPISA
2
C: Fluoroacetate dehalogenase
D: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2775
Polymers68,1472
Non-polymers1303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-40 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.230, 122.700, 132.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fluoroacetate dehalogenase


Mass: 34073.660 Da / Num. of mol.: 4
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1039 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-20% PEG3350, 0.2M NH4Cl, 0.1M sodium cacodylate. Microseeded using parent crystals grown with the supplementation of 4% sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9785646 Å
DetectorDate: Aug 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785646 Å / Relative weight: 1
ReflectionResolution: 1.55→90.17 Å / Num. obs: 189118 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.758 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.95
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.590.4853.336711513867199.8
1.59-1.630.40446589313559199.8
1.63-1.680.3214.966393413156199.9
1.68-1.730.2596.086211112748199.8
1.73-1.790.2047.616062112434199.8
1.79-1.850.1579.515850611964199.8
1.85-1.920.11712.015687611647199.8
1.92-20.08715.335452811160199.8
2-2.090.0718.55222710688199.8
2.09-2.190.05921.455004510266199.8
2.19-2.310.05124.15475739775199.8
2.31-2.450.04526.41448759255199.8
2.45-2.620.04128.71419528687199.6
2.62-2.830.0430.8391928112199.6
2.83-3.10.07134.85608947514199.7
3.1-3.470.06638.296483168291100
3.47-40.05841.1577856031199.9
4-4.90.05241.94490105144199.5
4.9-6.930.05241.29377934001199

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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: 1.6→90.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.688 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 8616 5 %RANDOM
Rwork0.1702 ---
obs0.1718 172070 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.4 Å2 / Biso mean: 21.1938 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→90.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9452 0 7 1039 10498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0219966
X-RAY DIFFRACTIONr_bond_other_d0.0010.026840
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.94113597
X-RAY DIFFRACTIONr_angle_other_deg1.123316490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43751227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97622.611471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.982151493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3571578
X-RAY DIFFRACTIONr_chiral_restr0.1460.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02111335
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022207
X-RAY DIFFRACTIONr_mcbond_it1.4011.56092
X-RAY DIFFRACTIONr_mcbond_other0.4691.52427
X-RAY DIFFRACTIONr_mcangle_it2.18429749
X-RAY DIFFRACTIONr_scbond_it3.12333874
X-RAY DIFFRACTIONr_scangle_it4.7334.53848
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 595 -
Rwork0.262 12013 -
all-12608 -
obs--99.78 %

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