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- PDB-3r3z: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/... -

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Basic information

Entry
Database: PDB / ID: 3r3z
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/Glycolate
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / FAcD / Defluorinase / Alpha/beta Hydrolase
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity / epoxide hydrolase 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 / NICKEL (II) ION / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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)136,77511
Polymers136,2954
Non-polymers4807
Water19,2401068
1
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4176
Polymers68,1472
Non-polymers2694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-22 kcal/mol
Surface area21590 Å2
MethodPISA
2
C: Fluoroacetate dehalogenase
D: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3585
Polymers68,1472
Non-polymers2113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-15 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.080, 122.120, 132.460
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 / Haloacetate 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-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O3
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1068 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
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: 14-BM-C / Wavelength: 0.9002 Å
DetectorDate: Aug 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.57→89.8 Å / Num. obs: 177077 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.041 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.57-1.610.6842.244348510540178.6
1.61-1.650.5762.945666112297194.4
1.65-1.70.473.726144912458197.8
1.7-1.750.3624.715942712078198.1
1.75-1.810.2885.775796111745198.2
1.81-1.870.2067.565611011388198.3
1.87-1.940.1579.425411211030198.5
1.94-2.020.11212.095207010595198.6
2.02-2.110.08514.515008610242198.5
2.11-2.210.06816.74480089836199
2.21-2.330.06618.82485629273199
2.33-2.470.10222.26797148889199.1
2.47-2.650.09325.21813848338199.2
2.65-2.860.07828.74760797817199.2
2.86-3.130.05935.42691927185199.4
3.13-3.50.04845.42622426556199.5
3.5-4.040.04255.37539955805199.6
4.04-4.950.03862.14443364960199.7
4.95-70.04154.56345133898199.7

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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: 1.7→18.23 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.097 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 7083 5 %RANDOM
Rwork0.1766 ---
obs0.1787 141042 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.36 Å2 / Biso mean: 17.8022 Å2 / Biso min: 3.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9458 0 23 1068 10549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0219934
X-RAY DIFFRACTIONr_bond_other_d0.0010.026818
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.94213542
X-RAY DIFFRACTIONr_angle_other_deg1.067316427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4151221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16322.57467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.832151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6791578
X-RAY DIFFRACTIONr_chiral_restr0.1310.21373
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111285
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022198
X-RAY DIFFRACTIONr_mcbond_it1.2971.56066
X-RAY DIFFRACTIONr_mcbond_other0.4441.52417
X-RAY DIFFRACTIONr_mcangle_it2.06929705
X-RAY DIFFRACTIONr_scbond_it3.08933868
X-RAY DIFFRACTIONr_scangle_it4.6544.53837
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 501 -
Rwork0.298 9741 -
all-10242 -
obs--98.01 %

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