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- PDB-5xc5: Crystal structure of Acanthamoeba polyphaga mimivirus Rab GTPase ... -

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Basic information

Entry
Database: PDB / ID: 5xc5
TitleCrystal structure of Acanthamoeba polyphaga mimivirus Rab GTPase in complex with GTP
ComponentsProbable Rab-related GTPase
KeywordsPROTEIN TRANSPORT / Rab GTPase / Acanthamoeba polyphaga mimivirus / vesicle trafficking
Function / homology
Function and homology information


protein transport / GTPase activity / GTP binding / host cell plasma membrane / membrane
Similarity search - Function
ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-TRIPHOSPHATE / Probable Rab-related GTPase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsKu, B. / You, J.A. / Kim, S.J.
CitationJournal: Arch. Virol. / Year: 2017
Title: Crystal structures of two forms of the Acanthamoeba polyphaga mimivirus Rab GTPase
Authors: Ku, B. / You, J.A. / Oh, K.J. / Yun, H.Y. / Lee, H.S. / Shin, H.C. / Jung, J. / Shin, Y.B. / Kim, S.J.
History
DepositionMar 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Probable Rab-related GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9206
Polymers20,1951
Non-polymers7255
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-14 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.924, 53.724, 96.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable Rab-related GTPase


Mass: 20194.979 Da / Num. of mol.: 1 / Fragment: UNP residues 9-184 / Mutation: Q65L
Source method: isolated from a genetically manipulated source
Details: Q65L mutation is introduced to impair the GTPase activity of this protein.
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UQ27
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium nitrate, 20%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.398→50 Å / Num. obs: 33149 / % possible obs: 98.4 % / Redundancy: 5.2 % / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XC3

5xc3


Resolution: 1.398→31.16 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 16.84
RfactorNum. reflection% reflection
Rfree0.1902 2000 6.03 %
Rwork0.1738 --
obs0.1748 33149 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.398→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 45 195 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061421
X-RAY DIFFRACTIONf_angle_d0.9761923
X-RAY DIFFRACTIONf_dihedral_angle_d21.638516
X-RAY DIFFRACTIONf_chiral_restr0.086213
X-RAY DIFFRACTIONf_plane_restr0.004238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3985-1.43340.20381100.19991715X-RAY DIFFRACTION74
1.4334-1.47220.23051220.20391901X-RAY DIFFRACTION84
1.4722-1.51550.20391380.19852142X-RAY DIFFRACTION93
1.5155-1.56440.19561420.18392210X-RAY DIFFRACTION96
1.5644-1.62030.2251430.17822226X-RAY DIFFRACTION97
1.6203-1.68520.19861430.17952242X-RAY DIFFRACTION98
1.6852-1.76190.20741480.18542296X-RAY DIFFRACTION99
1.7619-1.85480.20511460.1842279X-RAY DIFFRACTION98
1.8548-1.9710.1911480.17932302X-RAY DIFFRACTION99
1.971-2.12310.20191480.17012298X-RAY DIFFRACTION100
2.1231-2.33670.17211500.17142341X-RAY DIFFRACTION100
2.3367-2.67470.19731490.17582328X-RAY DIFFRACTION99
2.6747-3.36920.20221530.16692380X-RAY DIFFRACTION100
3.3692-31.16740.16191600.1632489X-RAY DIFFRACTION99

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