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

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Basic information

Entry
Database: PDB / ID: 6qhp
TitleTime resolved structural analysis of the full turnover of an enzyme - 2256 ms covalent intermediate 1
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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)68,3614
Polymers68,2052
Non-polymers1562
Water4,990277
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 area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.400, 78.670, 83.590
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


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
#2: 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
#3: Chemical ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3FO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 36.82 %
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.

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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 PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 1.75→81.54 Å / Num. obs: 48230 / % possible obs: 99.9 % / Redundancy: 24 % / Net I/σ(I): 4.5
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 48238
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r3u

3r3u


Resolution: 1.8→19.924 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.15
RfactorNum. reflection% reflection
Rfree0.266 2383 4.94 %
Rwork0.2178 --
obs0.2203 48230 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 10 277 4998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164972
X-RAY DIFFRACTIONf_angle_d1.5356789
X-RAY DIFFRACTIONf_dihedral_angle_d15.4224018
X-RAY DIFFRACTIONf_chiral_restr0.076698
X-RAY DIFFRACTIONf_plane_restr0.01891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83670.32381260.23432615X-RAY DIFFRACTION98
1.8367-1.87660.30711350.23182661X-RAY DIFFRACTION98
1.8766-1.92020.3091060.22682648X-RAY DIFFRACTION98
1.9202-1.96820.26731230.2182737X-RAY DIFFRACTION99
1.9682-2.02140.27791530.21072651X-RAY DIFFRACTION100
2.0214-2.08080.27521270.2172719X-RAY DIFFRACTION100
2.0808-2.14790.2951590.20812666X-RAY DIFFRACTION100
2.1479-2.22460.2711480.1982700X-RAY DIFFRACTION100
2.2246-2.31350.26181230.20072743X-RAY DIFFRACTION100
2.3135-2.41860.24311450.20152699X-RAY DIFFRACTION100
2.4186-2.54590.28591410.19842702X-RAY DIFFRACTION100
2.5459-2.70510.26131600.19722674X-RAY DIFFRACTION100
2.7051-2.91330.26221350.21042714X-RAY DIFFRACTION100
2.9133-3.20540.23651530.21122715X-RAY DIFFRACTION100
3.2054-3.66670.24941570.21512695X-RAY DIFFRACTION100
3.6667-4.61030.25491280.2122761X-RAY DIFFRACTION100
4.6103-19.9250.27971640.26432747X-RAY DIFFRACTION100

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