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- PDB-7a43: Fluoroacetate Dehalogenase measured by serial femtosecond crystal... -

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Basic information

Entry
Database: PDB / ID: 7a43
TitleFluoroacetate Dehalogenase measured by serial femtosecond crystallography
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / dehalogenase / serial femtosecond crystallography
Function / homologyhaloacetate dehalogenase / haloacetate dehalogenase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Fluoroacetate dehalogenase
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMehrabi, P. / Schulz, E.C. / Buecker, R.
CitationJournal: Sci Adv / Year: 2021
Title: Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison.
Authors: Mehrabi, P. / Bucker, R. / Bourenkov, G. / Ginn, H.M. / von Stetten, D. / Muller-Werkmeister, H.M. / Kuo, A. / Morizumi, T. / Eger, B.T. / Ou, W.L. / Oghbaey, S. / Sarracini, A. / Besaw, J.E. ...Authors: Mehrabi, P. / Bucker, R. / Bourenkov, G. / Ginn, H.M. / von Stetten, D. / Muller-Werkmeister, H.M. / Kuo, A. / Morizumi, T. / Eger, B.T. / Ou, W.L. / Oghbaey, S. / Sarracini, A. / Besaw, J.E. / Pare-Labrosse, O. / Meier, S. / Schikora, H. / Tellkamp, F. / Marx, A. / Sherrell, D.A. / Axford, D. / Owen, R.L. / Ernst, O.P. / Pai, E.F. / Schulz, E.C. / Miller, R.J.D.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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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)68,2184
Polymers68,1472
Non-polymers712
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-39 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.900, 79.900, 84.800
Angle α, β, γ (deg.)90.000, 103.400, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 18-20 % (w/v)) 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: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.22 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22 Å / Relative weight: 1
ReflectionResolution: 1.75→33.08 Å / Num. obs: 54828 / % possible obs: 100 % / Redundancy: 101.92 % / Biso Wilson estimate: 13.67 Å2 / CC1/2: 0.931 / Net I/σ(I): 3.88
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 5457 / CC1/2: 0.7232
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r3u

3r3u


Resolution: 1.75→33.08 Å / SU ML: 0.1765 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.2307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1995 1838 3.45 %
Rwork0.1627 51367 -
obs0.164 53205 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.53 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 2 306 4998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01164902
X-RAY DIFFRACTIONf_angle_d1.2526685
X-RAY DIFFRACTIONf_chiral_restr0.0674685
X-RAY DIFFRACTIONf_plane_restr0.0089881
X-RAY DIFFRACTIONf_dihedral_angle_d36.4544665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.26781300.2253588X-RAY DIFFRACTION88.9
1.8-1.850.24281290.20793693X-RAY DIFFRACTION91.44
1.85-1.910.2631430.18333844X-RAY DIFFRACTION93.92
1.91-1.980.26331460.17483867X-RAY DIFFRACTION96.17
1.98-2.060.21091420.17133917X-RAY DIFFRACTION96.67
2.06-2.150.21721360.16723987X-RAY DIFFRACTION98
2.15-2.260.19731410.15584005X-RAY DIFFRACTION98.71
2.26-2.410.19241390.1564042X-RAY DIFFRACTION99.26
2.41-2.590.20971410.16234058X-RAY DIFFRACTION99.2
2.59-2.850.19061460.16834049X-RAY DIFFRACTION99.5
2.85-3.260.19411470.16224071X-RAY DIFFRACTION99.74
3.27-4.110.17221480.1424091X-RAY DIFFRACTION99.95
4.11-33.080.1661500.15264155X-RAY DIFFRACTION99.88

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