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- PDB-8xtu: Crystal Structure of Rab5b GTPase domain from Leishmania donovani... -

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Basic information

Entry
Database: PDB / ID: 8xtu
TitleCrystal Structure of Rab5b GTPase domain from Leishmania donovani in complex with GDP
ComponentsRab5
KeywordsENDOCYTOSIS / GTPase / Early Endocytosis / Nucleotide Exchange
Function / homology
Function and homology information


vesicle-mediated transport / phagocytic vesicle membrane / early endosome / GTPase activity / GTP binding
Similarity search - Function
: / Small GTPase Rab domain profile. / Small GTPase Ras domain 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Rab5
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)CSIR NCP MLP 2031 India
CitationJournal: To Be Published
Title: Crystal Structure of Rab5b GTPase domain from Leishmania donovani in complex with GDP
Authors: Zohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A.
History
DepositionJan 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9453
Polymers18,4781
Non-polymers4682
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size Exclusion Chromatography purification was done
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.066, 61.861, 73.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein Rab5


Mass: 18477.748 Da / Num. of mol.: 1 / Mutation: C62S, Q80L, C151S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VN21
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Sodium Acetate, MES Hydrate pH 6.7, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 2.5→47.4 Å / Num. obs: 6617 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.996 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 739 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.36 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 41.131 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26324 620 9.4 %RANDOM
Rwork0.21575 ---
obs0.22038 5947 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.442 Å2
Baniso -1Baniso -2Baniso -3
1-10.8 Å2-0 Å20 Å2
2---5.89 Å2-0 Å2
3----4.92 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 29 33 1195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121182
X-RAY DIFFRACTIONr_bond_other_d0.0060.0161052
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.6411598
X-RAY DIFFRACTIONr_angle_other_deg0.8711.5742394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.85755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15510154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021379
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02275
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.094.042621
X-RAY DIFFRACTIONr_mcbond_other5.0884.041621
X-RAY DIFFRACTIONr_mcangle_it8.1547.244771
X-RAY DIFFRACTIONr_mcangle_other8.1517.243772
X-RAY DIFFRACTIONr_scbond_it4.7584.253561
X-RAY DIFFRACTIONr_scbond_other4.7564.254561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.67.784828
X-RAY DIFFRACTIONr_long_range_B_refined14.40563.944818
X-RAY DIFFRACTIONr_long_range_B_other14.37663.944818
X-RAY DIFFRACTIONr_rigid_bond_restr1.93332234
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 51 -
Rwork0.363 412 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -18.2813 Å / Origin y: -16.4254 Å / Origin z: 7.7169 Å
111213212223313233
T0.049 Å2-0.0254 Å2-0.021 Å2-0.0413 Å20.0157 Å2--0.0101 Å2
L0.6907 °2-1.4788 °2-0.5971 °2-5.8412 °21.5158 °2--4.963 °2
S0.0189 Å °0.1237 Å °0.0146 Å °-0.3614 Å °-0.0494 Å °0.125 Å °-0.1777 Å °0.0044 Å °0.0305 Å °

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