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- PDB-6qkw: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Tyr... -

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Basic information

Entry
Database: PDB / ID: 6qkw
TitleCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Tyr219Phe - Fluoroacetate soaked 2hr
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / Hydrolaser / Substrate Inhibition / Allostery / Dynamics
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
fluoroacetic acid / GLYCOLIC ACID / Fluoroacetate dehalogenase / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / Resolution: 1.512 Å
AuthorsMehrabi, P. / Kim, T.H. / Prosser, R.S. / Pai, E.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Substrate-Based Allosteric Regulation of a Homodimeric Enzyme.
Authors: Mehrabi, P. / Di Pietrantonio, C. / Kim, T.H. / Sljoka, A. / Taverner, K. / Ing, C. / Kruglyak, N. / Pomes, R. / Pai, E.F. / Prosser, R.S.
History
DepositionJan 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_nonpoly_scheme / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
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

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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)68,3836
Polymers68,1152
Non-polymers2684
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-25 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.750, 79.370, 85.010
Angle α, β, γ (deg.)90.00, 103.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 34057.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPYSC3_11920 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R4GQN1, UniProt: Q6NAM1*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3FO2
#4: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18-20% PEG3350, 200 mM CaCl2, and 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.512→28.653 Å / Num. obs: 81991 / % possible obs: 97.21 % / Redundancy: 3.3 % / Net I/σ(I): 25.51
Reflection shellResolution: 1.512→1.566 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.512→28.653 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.1952 4072 4.97 %
Rwork0.1686 --
obs0.17 81991 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.512→28.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 16 652 5350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014938
X-RAY DIFFRACTIONf_angle_d1.1376735
X-RAY DIFFRACTIONf_dihedral_angle_d15.7853948
X-RAY DIFFRACTIONf_chiral_restr0.079685
X-RAY DIFFRACTIONf_plane_restr0.008889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.512-1.52980.2462800.21141857X-RAY DIFFRACTION67
1.5298-1.54850.25661390.21392636X-RAY DIFFRACTION95
1.5485-1.56810.23411360.20222622X-RAY DIFFRACTION97
1.5681-1.58870.23821250.19972706X-RAY DIFFRACTION97
1.5887-1.61050.23121350.19672726X-RAY DIFFRACTION98
1.6105-1.63350.26091520.18952653X-RAY DIFFRACTION98
1.6335-1.65780.22031400.18772724X-RAY DIFFRACTION98
1.6578-1.68370.24361330.18122718X-RAY DIFFRACTION98
1.6837-1.71130.20541560.17982685X-RAY DIFFRACTION99
1.7113-1.74090.22951470.18142698X-RAY DIFFRACTION98
1.7409-1.77250.21671450.18322697X-RAY DIFFRACTION98
1.7725-1.80660.20871310.17772718X-RAY DIFFRACTION98
1.8066-1.84350.19681440.17372689X-RAY DIFFRACTION98
1.8435-1.88350.18191220.17612743X-RAY DIFFRACTION98
1.8835-1.92730.20121440.17412676X-RAY DIFFRACTION98
1.9273-1.97550.21741420.17322728X-RAY DIFFRACTION98
1.9755-2.02890.18511460.16892715X-RAY DIFFRACTION99
2.0289-2.08860.1971530.17832723X-RAY DIFFRACTION98
2.0886-2.1560.21931280.17092675X-RAY DIFFRACTION99
2.156-2.2330.21621430.16622737X-RAY DIFFRACTION98
2.233-2.32240.19551650.17672686X-RAY DIFFRACTION97
2.3224-2.42810.20981450.16842721X-RAY DIFFRACTION99
2.4281-2.5560.21011420.17632727X-RAY DIFFRACTION99
2.556-2.7160.23361440.17032724X-RAY DIFFRACTION99
2.716-2.92550.1811490.17412767X-RAY DIFFRACTION100
2.9255-3.21960.17091510.16652780X-RAY DIFFRACTION100
3.2196-3.68460.18581420.15292750X-RAY DIFFRACTION100
3.6846-4.63910.13321440.12892821X-RAY DIFFRACTION100
4.6391-28.65860.15881490.15312817X-RAY DIFFRACTION100

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