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

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Basic information

Entry
Database: PDB / ID: 6qht
TitleTime resolved structural analysis of the full turnover of an enzyme - 376 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: 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
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)68,2253
Polymers68,1472
Non-polymers781
Water8,089449
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 area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 78.630, 83.530
Angle α, β, γ (deg.)90.00, 102.79, 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.: 449 / 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 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→81.47 Å / Num. obs: 53488 / % possible obs: 98 % / Redundancy: 40.2 % / CC1/2: 0.943 / Net I/σ(I): 5.7
Reflection shellResolution: 1.73→1.83 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→19.993 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.83
RfactorNum. reflection% reflection
Rfree0.2084 2637 4.93 %
Rwork0.1678 --
obs0.1699 53488 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4717 0 5 449 5171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145004
X-RAY DIFFRACTIONf_angle_d1.436850
X-RAY DIFFRACTIONf_dihedral_angle_d15.1344048
X-RAY DIFFRACTIONf_chiral_restr0.07714
X-RAY DIFFRACTIONf_plane_restr0.009899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7283-1.75970.3808810.34561688X-RAY DIFFRACTION63
1.7597-1.79350.32341460.26872710X-RAY DIFFRACTION100
1.7935-1.83010.2861270.21592732X-RAY DIFFRACTION100
1.8301-1.86990.25981430.19772722X-RAY DIFFRACTION100
1.8699-1.91340.23831060.18512738X-RAY DIFFRACTION100
1.9134-1.96120.22981290.17262760X-RAY DIFFRACTION100
1.9612-2.01410.24161560.17352681X-RAY DIFFRACTION100
2.0141-2.07340.21261220.16952766X-RAY DIFFRACTION100
2.0734-2.14020.21021570.16572679X-RAY DIFFRACTION100
2.1402-2.21660.20071550.16172714X-RAY DIFFRACTION100
2.2166-2.30520.2331210.16432762X-RAY DIFFRACTION100
2.3052-2.410.21611500.16532729X-RAY DIFFRACTION100
2.41-2.53680.2491390.15972714X-RAY DIFFRACTION100
2.5368-2.69540.19811590.16222692X-RAY DIFFRACTION100
2.6954-2.90290.21211400.16182757X-RAY DIFFRACTION100
2.9029-3.1940.20171560.1582738X-RAY DIFFRACTION100
3.194-3.65370.17651550.14432712X-RAY DIFFRACTION100
3.6537-4.59410.15781310.14512788X-RAY DIFFRACTION100
4.5941-19.99440.19421640.17742769X-RAY DIFFRACTION100

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