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

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Basic information

Entry
Database: PDB / ID: 6qhu
TitleTime resolved structural analysis of the full turnover of an enzyme - 100 ms
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / time-resolved / catalysis / intermediate
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: 1.73 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
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-18 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.370, 78.630, 83.540
Angle α, β, γ (deg.)90.00, 102.74, 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)
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 36.75 %
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 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.73→81.5 Å / Num. obs: 53372 / % possible obs: 98.1 % / Redundancy: 43.1 % / CC1/2: 0.942 / Net I/σ(I): 8.1
Reflection shellResolution: 1.73→1.84 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: 1.73→19.997 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.55
RfactorNum. reflection% reflection
Rfree0.2067 2639 4.94 %
Rwork0.1663 --
obs0.1683 53372 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 5 459 5163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145014
X-RAY DIFFRACTIONf_angle_d1.4656865
X-RAY DIFFRACTIONf_dihedral_angle_d14.5875110
X-RAY DIFFRACTIONf_chiral_restr0.074708
X-RAY DIFFRACTIONf_plane_restr0.01906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7304-1.76190.412940.33231711X-RAY DIFFRACTION64
1.7619-1.79580.31231380.26032718X-RAY DIFFRACTION100
1.7958-1.83240.25261290.20232709X-RAY DIFFRACTION100
1.8324-1.87220.23541440.18392724X-RAY DIFFRACTION100
1.8722-1.91570.24281080.17622726X-RAY DIFFRACTION100
1.9157-1.96360.23481300.16942769X-RAY DIFFRACTION100
1.9636-2.01660.20731510.16562654X-RAY DIFFRACTION100
2.0166-2.07590.23041210.16522763X-RAY DIFFRACTION100
2.0759-2.14280.2331600.16092657X-RAY DIFFRACTION100
2.1428-2.21930.20671530.16032703X-RAY DIFFRACTION100
2.2193-2.30810.25041210.16642766X-RAY DIFFRACTION100
2.3081-2.41290.23411480.15812717X-RAY DIFFRACTION100
2.4129-2.53990.22971390.15622714X-RAY DIFFRACTION100
2.5399-2.69870.19631620.15832693X-RAY DIFFRACTION100
2.6987-2.90650.21171380.15422730X-RAY DIFFRACTION100
2.9065-3.19790.19271530.15672733X-RAY DIFFRACTION100
3.1979-3.65820.18221570.14532705X-RAY DIFFRACTION100
3.6582-4.59970.14141290.15092780X-RAY DIFFRACTION100
4.5997-19.99850.1911640.18212761X-RAY DIFFRACTION100

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