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

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Basic information

Entry
Database: PDB / ID: 6gxd
TitleThe hit-and-return system enables efficient time-resolved serial synchrotron crystallography: FAcD752MS 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 (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: 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)68,2965
Polymers68,1472
Non-polymers1493
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-28 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.370, 78.540, 83.510
Angle α, β, γ (deg.)90.00, 102.76, 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 (phototrophic)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 36.65 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG 3350, 18-20 (w/v) CaCl2, 100 mM Tris HCl, 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 PILATUS3 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→81.5 Å / Num. obs: 48357 / % possible obs: 99.9 % / Redundancy: 39.5 % / Biso Wilson estimate: 18.74 Å2 / Net I/σ(I): 5.3
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→40.724 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 4.99 / Phase error: 20.79
RfactorNum. reflection% reflection
Rfree0.209 2388 4.94 %
Rwork0.1651 --
obs0.1673 48304 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 7 443 5164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164991
X-RAY DIFFRACTIONf_angle_d1.556824
X-RAY DIFFRACTIONf_dihedral_angle_d14.5284558
X-RAY DIFFRACTIONf_chiral_restr0.077705
X-RAY DIFFRACTIONf_plane_restr0.01899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83670.32931290.23982657X-RAY DIFFRACTION100
1.8367-1.87670.28081380.20612716X-RAY DIFFRACTION100
1.8767-1.92030.2251060.18122693X-RAY DIFFRACTION100
1.9203-1.96830.24731250.17622751X-RAY DIFFRACTION100
1.9683-2.02160.22211500.16462633X-RAY DIFFRACTION100
2.0216-2.0810.21381310.16422720X-RAY DIFFRACTION100
2.081-2.14820.22121650.16472662X-RAY DIFFRACTION100
2.1482-2.2250.21411380.16722690X-RAY DIFFRACTION100
2.225-2.31410.27551220.17152724X-RAY DIFFRACTION100
2.3141-2.41940.20251460.16212685X-RAY DIFFRACTION100
2.4194-2.54690.23551410.1662718X-RAY DIFFRACTION100
2.5469-2.70650.22761600.16162671X-RAY DIFFRACTION100
2.7065-2.91540.22671350.16082716X-RAY DIFFRACTION100
2.9154-3.20860.19751510.15572681X-RAY DIFFRACTION100
3.2086-3.67270.18811570.14962702X-RAY DIFFRACTION100
3.6727-4.62620.17681300.14772751X-RAY DIFFRACTION100
4.6262-40.73420.17811640.17852746X-RAY DIFFRACTION100

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