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- PDB-7a42: Fluoroacetate Dehalogenase measured by serial synchrotron crystal... -

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Basic information

Entry
Database: PDB / ID: 7a42
TitleFluoroacetate Dehalogenase measured by serial synchrotron crystallography
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / dehalogenase / serial synchrotron 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 / SYNCHROTRON / 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
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-38 kcal/mol
Surface area20380 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.: 300 / 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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.75→57.39 Å / Num. obs: 54827 / % possible obs: 100 % / Redundancy: 139.52 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 0.9534 / Net I/σ(I): 4.18
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 5456 / CC1/2: 0.5252
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: 0.1824 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.6975
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1929 1852 3.56 %
Rwork0.157 50212 -
obs0.1583 52064 94.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.87 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 2 300 5000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934955
X-RAY DIFFRACTIONf_angle_d1.08166761
X-RAY DIFFRACTIONf_chiral_restr0.06691
X-RAY DIFFRACTIONf_plane_restr0.0076893
X-RAY DIFFRACTIONf_dihedral_angle_d36.8255678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.32941150.29923217X-RAY DIFFRACTION79.67
1.8-1.850.30061240.2523469X-RAY DIFFRACTION85.87
1.85-1.910.22291330.2113676X-RAY DIFFRACTION89.79
1.91-1.980.24231380.18193738X-RAY DIFFRACTION92.91
1.98-2.060.2351380.17053880X-RAY DIFFRACTION95.69
2.06-2.150.20111480.15813927X-RAY DIFFRACTION96.89
2.15-2.260.20271470.15823963X-RAY DIFFRACTION97.81
2.26-2.410.21541470.15844005X-RAY DIFFRACTION98.58
2.41-2.590.20791510.16154025X-RAY DIFFRACTION98.65
2.59-2.850.20731560.16314027X-RAY DIFFRACTION99.05
2.85-3.270.19621460.1574053X-RAY DIFFRACTION99.41
3.27-4.110.14991530.1294080X-RAY DIFFRACTION99.79
4.12-57.390.1531560.13054152X-RAY DIFFRACTION99.86

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