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- PDB-6qhv: Time resolved structural analysis of the full turnover of an enzy... -

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Basic information

Entry
Database: PDB / ID: 6qhv
TitleTime resolved structural analysis of the full turnover of an enzyme - 100 ms
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / time-resolved / catalysis / intermediate
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
fluoroacetic acid / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.715 Å
AuthorsSchulz, E.C. / Mehrabi, P. / Pai, E.F. / Miller, D.
CitationJournal: Science / Year: 2019
Title: Time-resolved crystallography reveals allosteric communication aligned with molecular breathing.
Authors: Mehrabi, P. / Schulz, E.C. / Dsouza, R. / Muller-Werkmeister, H.M. / Tellkamp, F. / Miller, R.J.D. / Pai, E.F.
History
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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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
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-18 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.370, 78.580, 83.550
Angle α, β, γ (deg.)90.00, 102.73, 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 (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-FAH / fluoroacetic acid / 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 / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 36.72 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
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, DESY / Beamline: P11 / Wavelength: 1.0089 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.7→81.5 Å / Num. obs: 53598 / % possible obs: 96.1 % / Redundancy: 94.6 % / CC1/2: 0.974 / Net I/σ(I): 8.1
Reflection shellResolution: 1.72→1.82 Å
Serial crystallography sample deliveryDescription: chip / Method: fixed target

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Processing

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

3r3u


Resolution: 1.715→19.996 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.1935 2642 4.93 %
Rwork0.1609 --
obs0.1626 53598 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.715→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 5 374 5078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155021
X-RAY DIFFRACTIONf_angle_d1.4286876
X-RAY DIFFRACTIONf_dihedral_angle_d14.6315111
X-RAY DIFFRACTIONf_chiral_restr0.075709
X-RAY DIFFRACTIONf_plane_restr0.009908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7151-1.74630.3458340.3312650X-RAY DIFFRACTION23
1.7463-1.77980.35991370.25512794X-RAY DIFFRACTION100
1.7798-1.81610.23711430.1912755X-RAY DIFFRACTION100
1.8161-1.85560.23241400.17452798X-RAY DIFFRACTION100
1.8556-1.89870.2251220.16422797X-RAY DIFFRACTION100
1.8987-1.94620.21691140.15812808X-RAY DIFFRACTION100
1.9462-1.99880.20551640.15532775X-RAY DIFFRACTION100
1.9988-2.05750.18381220.14692816X-RAY DIFFRACTION100
2.0575-2.12390.2081520.15172766X-RAY DIFFRACTION100
2.1239-2.19970.18661710.14572779X-RAY DIFFRACTION100
2.1997-2.28760.18841240.1472812X-RAY DIFFRACTION100
2.2876-2.39160.21470.14992764X-RAY DIFFRACTION100
2.3916-2.51740.20611440.15242785X-RAY DIFFRACTION100
2.5174-2.67480.18471620.15642781X-RAY DIFFRACTION100
2.6748-2.88080.19741430.15842818X-RAY DIFFRACTION100
2.8808-3.16970.19931620.15852801X-RAY DIFFRACTION100
3.1697-3.6260.19021590.14772772X-RAY DIFFRACTION100
3.626-4.55940.15991360.15242841X-RAY DIFFRACTION100
4.5594-19.99760.17371660.18232844X-RAY DIFFRACTION100

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