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

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Basic information

Entry
Database: PDB / ID: 6qhw
TitleTime resolved structural analysis of the full turnover of an enzyme - 4512 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 / GLYCOLIC ACID / Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.718 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1

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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)68,3014
Polymers68,1472
Non-polymers1542
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-13 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 78.660, 83.570
Angle α, β, γ (deg.)90.00, 102.70, 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-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#3: Chemical ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3FO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 1.95 Å3/Da / Density % sol: 36.79 %
Crystal growTemperature: 293 K / Method: batch mode
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: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.718→81.53 Å / Num. obs: 53299 / % possible obs: 95.7 % / Redundancy: 36.6 % / Net I/σ(I): 5.2
Reflection shellResolution: 1.72→1.75 Å
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.718→19.993 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.58
RfactorNum. reflection% reflection
Rfree0.2257 2627 4.93 %
Rwork0.1848 --
obs0.1869 53299 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.718→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 10 451 5158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134887
X-RAY DIFFRACTIONf_angle_d1.2876656
X-RAY DIFFRACTIONf_dihedral_angle_d13.6353957
X-RAY DIFFRACTIONf_chiral_restr0.064685
X-RAY DIFFRACTIONf_plane_restr0.008873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7177-1.74890.4356300.3365557X-RAY DIFFRACTION20
1.7489-1.78260.34941390.28642755X-RAY DIFFRACTION100
1.7826-1.81890.29431430.23172765X-RAY DIFFRACTION100
1.8189-1.85840.27871340.20892785X-RAY DIFFRACTION100
1.8584-1.90160.2781180.19072793X-RAY DIFFRACTION100
1.9016-1.94920.26541210.18742788X-RAY DIFFRACTION100
1.9492-2.00180.23161580.18392775X-RAY DIFFRACTION100
2.0018-2.06070.22751260.17642808X-RAY DIFFRACTION100
2.0607-2.12710.2431550.1742754X-RAY DIFFRACTION100
2.1271-2.2030.22061630.16812758X-RAY DIFFRACTION100
2.203-2.29110.22311240.17042816X-RAY DIFFRACTION100
2.2911-2.39520.24111480.17182755X-RAY DIFFRACTION100
2.3952-2.52130.24111450.16962777X-RAY DIFFRACTION100
2.5213-2.67890.20571610.1722774X-RAY DIFFRACTION100
2.6789-2.88520.22941410.18112810X-RAY DIFFRACTION100
2.8852-3.17450.22081630.17752781X-RAY DIFFRACTION100
3.1745-3.63150.21671570.17632767X-RAY DIFFRACTION100
3.6315-4.56620.19181350.17652826X-RAY DIFFRACTION100
4.5662-19.99420.20531660.20562828X-RAY DIFFRACTION100

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