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

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Basic information

Entry
Database: PDB / ID: 6qhz
TitleTime resolved structural analysis of the full turnover of an enzyme - 6788 ms
Components(Fluoroacetate dehalogenase) x 2
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 / Resolution: 1.799 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 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)68,2833
Polymers68,2052
Non-polymers781
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-18 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 78.620, 83.540
Angle α, β, γ (deg.)90.00, 102.75, 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.: 1
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: Protein Fluoroacetate dehalogenase


Mass: 34131.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#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.: 479 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 36.67 %
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: 1.75→81.49 Å / Num. obs: 48443 / % possible obs: 99.8 % / Redundancy: 30.3 % / Net I/σ(I): 4.4
Reflection shellResolution: 1.79→1.83 Å
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.799→19.993 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.97
RfactorNum. reflection% reflection
Rfree0.2303 2392 4.94 %
Rwork0.1841 --
obs0.1864 48443 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.799→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 5 479 5187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174901
X-RAY DIFFRACTIONf_angle_d1.7036675
X-RAY DIFFRACTIONf_dihedral_angle_d15.0373959
X-RAY DIFFRACTIONf_chiral_restr0.077682
X-RAY DIFFRACTIONf_plane_restr0.011877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7987-1.83540.3211290.25652671X-RAY DIFFRACTION100
1.8354-1.87530.33821390.23742719X-RAY DIFFRACTION100
1.8753-1.91880.28841080.21682711X-RAY DIFFRACTION100
1.9188-1.96680.25391220.20132754X-RAY DIFFRACTION100
1.9668-2.01990.26791540.20072656X-RAY DIFFRACTION100
2.0199-2.07930.25721270.20222718X-RAY DIFFRACTION100
2.0793-2.14630.26161590.19312669X-RAY DIFFRACTION100
2.1463-2.22290.26021480.18672697X-RAY DIFFRACTION100
2.2229-2.31180.27241220.19062740X-RAY DIFFRACTION100
2.3118-2.41690.23751460.18512702X-RAY DIFFRACTION100
2.4169-2.54410.23741410.17722699X-RAY DIFFRACTION100
2.5441-2.70310.22451600.18332677X-RAY DIFFRACTION100
2.7031-2.91120.24141350.18132714X-RAY DIFFRACTION100
2.9112-3.20310.23141530.17332716X-RAY DIFFRACTION100
3.2031-3.66410.20241570.16332699X-RAY DIFFRACTION100
3.6641-4.60710.17171280.15982760X-RAY DIFFRACTION100
4.6071-19.99380.20781640.18942749X-RAY DIFFRACTION100

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