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- PDB-6fsx: The hit-and-return system enables efficient time-resolved serial ... -

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Basic information

Entry
Database: PDB / ID: 6fsx
TitleThe hit-and-return system enables efficient time-resolved serial synchrotron crystallography
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / halogenase
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
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchulz, E.C. / Mehrabi, P. / Mueller-werkmeiser, H. / Tellkamp, F. / Jha, A. / Stuart, W. / Persch, E. / De Gasparo, R. / Diederich, F. / Pai, E. / Miller, D.
CitationJournal: Nat. Methods / Year: 2018
Title: The hit-and-return system enables efficient time-resolved serial synchrotron crystallography.
Authors: Schulz, E.C. / Mehrabi, P. / Muller-Werkmeister, H.M. / Tellkamp, F. / Jha, A. / Stuart, W. / Persch, E. / De Gasparo, R. / Diederich, F. / Pai, E.F. / Miller, R.J.D.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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


Theoretical massNumber of molelcules
Total (without water)68,1472
Polymers68,1472
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-19 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.780, 79.380, 84.470
Angle α, β, γ (deg.)90.00, 102.88, 90.00
Int Tables number4
Space group name H-MP1211

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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 (strain ATCC BAA-98 / CGA009) (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 273 K / Method: batch mode
Details: (18-20 percent (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: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→82.46 Å / Num. obs: 49797 / % possible obs: 100 % / Redundancy: 268.3 % / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.83 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→82.345 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 5.03 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 1630 3.27 %
Rwork0.1692 --
obs0.1706 49794 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→82.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 0 248 4942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014953
X-RAY DIFFRACTIONf_angle_d1.1846761
X-RAY DIFFRACTIONf_dihedral_angle_d15.7733979
X-RAY DIFFRACTIONf_chiral_restr0.065687
X-RAY DIFFRACTIONf_plane_restr0.008891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.85280.2621250.19013903X-RAY DIFFRACTION98
1.8528-1.91260.22851390.17354022X-RAY DIFFRACTION100
1.9126-1.9810.22741370.16274002X-RAY DIFFRACTION100
1.981-2.06030.20721310.15763982X-RAY DIFFRACTION100
2.0603-2.15410.22551410.16053997X-RAY DIFFRACTION100
2.1541-2.26760.19391350.15384026X-RAY DIFFRACTION100
2.2676-2.40970.22151280.16194016X-RAY DIFFRACTION100
2.4097-2.59580.23721390.164007X-RAY DIFFRACTION100
2.5958-2.8570.21261360.17094035X-RAY DIFFRACTION100
2.857-3.27040.18271390.16824032X-RAY DIFFRACTION100
3.2704-4.12040.20311420.16564033X-RAY DIFFRACTION100
4.1204-82.43090.21281380.18434109X-RAY DIFFRACTION100

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