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- PDB-7re6: Crystal Structure of the brown dog tick (Rhipicephalus sanguineus... -

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Basic information

Entry
Database: PDB / ID: 7re6
TitleCrystal Structure of the brown dog tick (Rhipicephalus sanguineus) Arginine Kinase in absence of substrate or ligands
ComponentsArginine kinase
KeywordsTRANSFERASE / phosphotransferase / monomer / phosphagen
Biological speciesRhipicephalus sanguineus (brown dog tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsGomez-Yanes, A.C. / Garcia-Orozco, K.D. / Lopez-Zavala, A.A. / Sotelo-Mundo, R.R.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CF-2019-610264 Mexico
CitationJournal: Catalysts / Year: 2022
Title: The Arginine Kinase from the Tick Rhipicephalus sanguineus Is an Efficient Biocatalyst
Authors: Gomez-Yanes, A.C. / Moreno-Cordova, E.N. / Garcia-Orozco, K.D. / Laino, A. / Islas-Osuna, M.A. / Lopez-Zavala, A.A. / Valenzuela, J.G. / Sotelo-Mundo, R.R.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine kinase


Theoretical massNumber of molelcules
Total (without water)42,3271
Polymers42,3271
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.412, 61.410, 61.342
Angle α, β, γ (deg.)90.000, 96.557, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Arginine kinase


Mass: 42327.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus sanguineus (brown dog tick)
Production host: Escherichia coli (E. coli) / References: arginine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 7.8 / Details: 0.1 M bis-tris pH 6.5, 25% p/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19 Å / Relative weight: 1
ReflectionResolution: 1.53→35.82 Å / Num. obs: 52892 / % possible obs: 98 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.28 Å2 / CC1/2: 0.887 / Net I/σ(I): 8.38
Reflection shellResolution: 1.53→1.58 Å / Num. unique obs: 52890 / CC1/2: 0.887 / % possible all: 93.01

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AM1

4am1


Resolution: 1.53→35.82 Å / SU ML: 0.1319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1857 2530 4.79 %
Rwork0.1552 50254 -
obs0.1567 52784 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.24 Å2
Refinement stepCycle: LAST / Resolution: 1.53→35.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 0 381 3133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012809
X-RAY DIFFRACTIONf_angle_d1.15563786
X-RAY DIFFRACTIONf_chiral_restr0.0569416
X-RAY DIFFRACTIONf_plane_restr0.0105491
X-RAY DIFFRACTIONf_dihedral_angle_d5.5556379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.560.27171230.23052462X-RAY DIFFRACTION86.72
1.56-1.590.23241430.20012771X-RAY DIFFRACTION98.38
1.59-1.630.24171350.1952799X-RAY DIFFRACTION97.77
1.63-1.660.20471100.18582818X-RAY DIFFRACTION97.89
1.66-1.70.18151300.17372770X-RAY DIFFRACTION97.35
1.7-1.750.2151430.16892754X-RAY DIFFRACTION96.79
1.75-1.80.21891490.17842781X-RAY DIFFRACTION97.31
1.8-1.860.21771580.16882813X-RAY DIFFRACTION99.66
1.86-1.930.19151320.17032822X-RAY DIFFRACTION99.36
1.93-20.17921530.15742809X-RAY DIFFRACTION99.3
2-2.10.20271470.15182806X-RAY DIFFRACTION99.03
2.1-2.210.17261550.15212800X-RAY DIFFRACTION98.01
2.21-2.340.16881740.14812747X-RAY DIFFRACTION97.59
2.34-2.530.18511540.14652779X-RAY DIFFRACTION97.57
2.53-2.780.14991240.14572878X-RAY DIFFRACTION99.93
2.78-3.180.18431670.15252838X-RAY DIFFRACTION99.7
3.18-4.010.17171110.14142894X-RAY DIFFRACTION99.08
4.01-35.820.18881220.15262913X-RAY DIFFRACTION98.19

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