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- PDB-6l6o: Crystal structure of stabilized Rab5a GTPase domain from Leishman... -

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Basic information

Entry
Database: PDB / ID: 6l6o
TitleCrystal structure of stabilized Rab5a GTPase domain from Leishmania donovani
ComponentsRab5a
KeywordsENDOCYTOSIS / Intracellular trafficking / GTPase
Function / homology
Function and homology information


GTPase activity / GTP binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / small GTPase Rab1 family profile. / small GTPase Rho family profile. / small GTPase Ras 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 ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / small GTPase Rab1 family profile. / small GTPase Rho family profile. / small GTPase Ras 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-DIPHOSPHATE / Rab5a
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsArora, A. / Zohib, M. / Biswal, B.K. / Maheshwari, D. / Pal, R.K.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP007 India
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani.
Authors: Zohib, M. / Maheshwari, D. / Pal, R.K. / Freitag-Pohl, S. / Biswal, B.K. / Pohl, E. / Arora, A.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Rab5a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0015
Polymers19,3821
Non-polymers6194
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography purification was done using Superdex-75 10/300GL column (GE Healthcare, Chicago, IL)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-19 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.018, 58.018, 103.418
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rab5a /


Mass: 19382.002 Da / Num. of mol.: 1 / Mutation: P58D, P59G, Q92L, C107S
Source method: isolated from a genetically manipulated source
Details: residue 60-79 deletion / Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: Rab5a / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A109NYM0

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200mM Ammonium Acetate, 100mM Tris HCl, pH 8.5 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. obs: 19056 / % possible obs: 98.9 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.015 / Rrim(I) all: 0.059 / Χ2: 1.315 / Net I/σ(I): 16 / Num. measured all: 287720
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.868.80.74817010.9090.2230.7841.03489.7
1.86-1.9413.10.5718800.9880.1530.5911.199.8
1.94-2.0314.90.43118810.9810.1130.4461.178100
2.03-2.1314.90.31518940.9890.0830.3261.224100
2.13-2.27150.22418890.9930.0590.2311.271100
2.27-2.4415.40.14219220.9980.0370.1471.29100
2.44-2.6916.20.10419230.9980.0260.1071.354100
2.69-3.0817.10.06719310.9990.0170.0691.39100
3.08-3.8817.70.038196710.0090.0391.564100
3.88-35170.027206810.0070.0271.4699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEI

2hei


Resolution: 1.8→24.42 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.151 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 938 4.9 %RANDOM
Rwork0.165 ---
obs0.1669 18075 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.71 Å2 / Biso mean: 35.103 Å2 / Biso min: 21.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----2.29 Å2
Refinement stepCycle: final / Resolution: 1.8→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 39 124 1429
Biso mean--37.66 43.39 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131344
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171271
X-RAY DIFFRACTIONr_angle_refined_deg2.1461.6651827
X-RAY DIFFRACTIONr_angle_other_deg1.5371.5872940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6585173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02422.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27115233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.764159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021506
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
LS refinement shellResolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 55 -
Rwork0.374 1134 -
all-1189 -
obs--85.66 %
Refinement TLS params.Method: refined / Origin x: -23.061 Å / Origin y: 20.903 Å / Origin z: -13.316 Å
111213212223313233
T0.0227 Å20.0131 Å20.012 Å2-0.12 Å2-0.0061 Å2--0.032 Å2
L0.4433 °20.0042 °2-0.5223 °2-0.4654 °20.2046 °2--1.0121 °2
S-0.0259 Å °-0.1163 Å °0.0649 Å °-0.029 Å °0.0093 Å °0.0454 Å °0.0942 Å °0.144 Å °0.0166 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 175
2X-RAY DIFFRACTION1A201 - 203

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