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

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Basic information

Entry
Database: PDB / ID: 6gxf
TitleThe hit-and-return system enables efficient time-resolved serial synchrotron crystallography: RADDAM1
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / time-resolved crystallography / serial synchrotron crystallography (SSX) / Pump-probe experiment / structural enzymology
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
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchulz, E.C. / Mehrabi, P. / Mueller-Werkmeister, H. / Tellkamp, F. / Stuart, W. / Persch, E. / De Gasparo, R. / Diederich, F. / Pai, E.F. / Miller, R.J.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
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 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 1.2Jan 17, 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


Theoretical massNumber of molelcules
Total (without water)68,1472
Polymers68,1472
Non-polymers00
Water7,422412
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-18 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.320, 78.540, 83.560
Angle α, β, γ (deg.)90.00, 102.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase / Haloacetate dehalogenase


Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 1.94 Å3/Da / Density % sol: 36.57 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG 3350 18 - 20 % CaCl 200 mM TrisHCL 100 mM pH 8.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0089 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.8→81.42 Å / Num. obs: 48178 / % possible obs: 99.8 % / Redundancy: 9.2 % / Net I/σ(I): 2.9
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSnXDSdata reduction
XSCALEnXSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r3u

3r3u


Resolution: 1.8→40.722 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 5.05 / Phase error: 28.55
RfactorNum. reflection% reflection
Rfree0.269 2387 4.96 %
Rwork0.2219 --
obs0.2243 48165 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 0 412 5136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064904
X-RAY DIFFRACTIONf_angle_d0.826681
X-RAY DIFFRACTIONf_dihedral_angle_d15.8173974
X-RAY DIFFRACTIONf_chiral_restr0.046685
X-RAY DIFFRACTIONf_plane_restr0.005878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83670.36421390.30082600X-RAY DIFFRACTION98
1.8367-1.87670.34931610.27662682X-RAY DIFFRACTION100
1.8767-1.92030.31531450.24962650X-RAY DIFFRACTION100
1.9203-1.96830.30511560.24362714X-RAY DIFFRACTION100
1.9683-2.02160.28141460.2372628X-RAY DIFFRACTION100
2.0216-2.08110.29481420.23332716X-RAY DIFFRACTION100
2.0811-2.14820.28341640.23362652X-RAY DIFFRACTION100
2.1482-2.2250.29291420.22732675X-RAY DIFFRACTION100
2.225-2.31410.33041090.22732723X-RAY DIFFRACTION100
2.3141-2.41940.27891460.22952684X-RAY DIFFRACTION100
2.4194-2.54690.29541190.22672725X-RAY DIFFRACTION100
2.5469-2.70650.30411260.22742712X-RAY DIFFRACTION100
2.7065-2.91540.25411000.21992742X-RAY DIFFRACTION100
2.9154-3.20860.25841520.20822675X-RAY DIFFRACTION100
3.2086-3.67270.22641370.19282712X-RAY DIFFRACTION100
3.6727-4.62620.20461580.19442727X-RAY DIFFRACTION100
4.6262-40.73270.28181450.23392761X-RAY DIFFRACTION100

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