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

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Basic information

Entry
Database: PDB / ID: 6gxt
TitleThe hit-and-return system enables efficient time-resolved serial synchrotron crystallography: FAcD2052MS after reaction initiation
ComponentsFluoroacetate dehalogenase
KeywordsDNA BINDING PROTEIN / time-resolved crystallography / serial synchrotron crystallography (SSX) / Pump-probe experiment / structural enzymology
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
fluoroacetic acid / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)68,2253
Polymers68,1472
Non-polymers781
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-18 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.760, 79.540, 84.460
Angle α, β, γ (deg.)90.00, 102.94, 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 CGA009 (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3FO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
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, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.96269 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96269 Å / Relative weight: 1
ReflectionResolution: 1.95→57.51 Å / Num. obs: 39351 / % possible obs: 99.9 % / Redundancy: 59.2 % / Net I/σ(I): 4
Reflection shellResolution: 1.95→2 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: 1.95→57.199 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 5.47 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2277 1863 4.73 %
Rwork0.1815 --
obs0.1836 39350 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→57.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 5 186 4895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084926
X-RAY DIFFRACTIONf_angle_d0.9056716
X-RAY DIFFRACTIONf_dihedral_angle_d15.8063966
X-RAY DIFFRACTIONf_chiral_restr0.05683
X-RAY DIFFRACTIONf_plane_restr0.006885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9493-2.0020.33891450.2562869X-RAY DIFFRACTION99
2.002-2.06090.30471320.23482851X-RAY DIFFRACTION100
2.0609-2.12740.29781620.22172856X-RAY DIFFRACTION100
2.1274-2.20350.28581370.21022895X-RAY DIFFRACTION100
2.2035-2.29170.29971440.20712846X-RAY DIFFRACTION100
2.2917-2.3960.25521670.19942849X-RAY DIFFRACTION100
2.396-2.52230.29441410.20032876X-RAY DIFFRACTION100
2.5223-2.68030.24871240.18992898X-RAY DIFFRACTION100
2.6803-2.88730.21481430.17892879X-RAY DIFFRACTION100
2.8873-3.17780.24371420.18122910X-RAY DIFFRACTION100
3.1778-3.63760.18631210.16182908X-RAY DIFFRACTION100
3.6376-4.58270.19141680.14962884X-RAY DIFFRACTION100
4.5827-57.22380.18081370.17332966X-RAY DIFFRACTION100

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