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- PDB-8jqu: Crystal structure of GppNHp bound GTPase domain of Rab5a from Lei... -

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Basic information

Entry
Database: PDB / ID: 8jqu
TitleCrystal structure of GppNHp bound GTPase domain of Rab5a from Leishmania donovani
ComponentsRab5a
KeywordsENDOCYTOSIS / Early Endocytosis / GTPase / Active conformation
Function / homology
Function and homology information


vesicle-mediated transport / endosome / GTPase activity / GTP binding / metal ion 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rab5a
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsPandey, D. / Zohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A.
Funding support India, United Kingdom, 2items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)CSIR NCP MLP2031 India
Global Challenges Research FundMR/P027989/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of GppNHp bound GTPase domain of Rab5a from Leishmania donovani
Authors: Pandey, D. / Zohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A.
History
DepositionJun 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab5a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8464
Polymers19,2381
Non-polymers6093
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size Exclusion Chromatography experiment was done
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.552, 42.266, 37.777
Angle α, β, γ (deg.)90.000, 103.387, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-438-

HOH

21A-441-

HOH

31A-462-

HOH

41A-486-

HOH

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Components

#1: Protein Rab5a


Mass: 19237.873 Da / Num. of mol.: 1
Mutation: P58D, P59G, 60-79 residue deletion, Q93L, C107S, 196-235 residue deletion
Source method: isolated from a genetically manipulated source
Details: GppNHp / Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: Rab5a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A109NYM0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Magnesium Acetate, 0.1M Tris-HCl pH 8.5, 19% PEG 8K

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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 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.798→35 Å / Num. obs: 15882 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rrim(I) all: 0.054 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.865.60.2215320.9750.9940.10.2421.14897.7
1.86-1.946.50.17715620.9850.9960.0750.1931.22699.6
1.94-2.036.50.13515970.9890.9970.0570.1471.40299.9
2.03-2.136.60.10615670.9940.9980.0440.1151.58100
2.13-2.276.70.08715950.9950.9990.0360.0941.767100
2.27-2.446.70.07215800.9960.9990.030.0791.948100
2.44-2.696.70.06216060.9970.9990.0260.0682.096100
2.69-3.086.80.0515870.9980.9990.0210.0552.131100
3.08-3.886.80.0416100.99910.0170.0432.2100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.798→27.354 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.163 / SU B: 4.253 / SU ML: 0.075 / Average fsc free: 0.9411 / Average fsc work: 0.9525 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2029 793 4.993 %
Rwork0.1616 15089 -
all0.164 --
obs-15882 99.449 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.248 Å2
2--0.152 Å2-0 Å2
3----0.278 Å2
Refinement stepCycle: LAST / Resolution: 1.798→27.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 37 190 1462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0121313
X-RAY DIFFRACTIONr_angle_refined_deg2.131.6381786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58222.75958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70315219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.837157
X-RAY DIFFRACTIONr_chiral_restr0.1530.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02977
X-RAY DIFFRACTIONr_nbd_refined0.2390.2639
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2152
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.216
X-RAY DIFFRACTIONr_mcbond_it2.5532.345666
X-RAY DIFFRACTIONr_mcangle_it3.9013.499834
X-RAY DIFFRACTIONr_scbond_it3.3852.469647
X-RAY DIFFRACTIONr_scangle_it5.1043.573948
X-RAY DIFFRACTIONr_lrange_it7.14231.9332117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.8450.278610.2351038X-RAY DIFFRACTION93.9316
1.845-1.8950.223580.2061093X-RAY DIFFRACTION100
1.895-1.950.221430.181040X-RAY DIFFRACTION99.449
1.95-2.010.195660.1521023X-RAY DIFFRACTION99.9083
2.01-2.0760.185560.147981X-RAY DIFFRACTION100
2.076-2.1490.17410.152952X-RAY DIFFRACTION100
2.149-2.230.207390.161964X-RAY DIFFRACTION100
2.23-2.320.259390.157899X-RAY DIFFRACTION100
2.32-2.4230.216370.169861X-RAY DIFFRACTION100
2.423-2.5420.203420.16829X-RAY DIFFRACTION100
2.542-2.6790.2410.163773X-RAY DIFFRACTION100
2.679-2.8410.229430.168759X-RAY DIFFRACTION100
2.841-3.0360.198290.17689X-RAY DIFFRACTION100
3.036-3.2790.257360.164657X-RAY DIFFRACTION100
3.279-3.590.178290.15594X-RAY DIFFRACTION100
3.59-4.0120.168580.134526X-RAY DIFFRACTION100
4.012-4.6280.145320.133479X-RAY DIFFRACTION100
4.628-5.6580.214230.149407X-RAY DIFFRACTION100
5.658-7.9570.302150.216333X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.2979 Å / Origin y: 14.6012 Å / Origin z: 11.8288 Å
111213212223313233
T0.004 Å2-0.0004 Å2-0.0021 Å2-0.0051 Å20.001 Å2--0.0022 Å2
L0.3406 °20.1126 °2-0.0024 °2-0.2664 °2-0.0189 °2--0.302 °2
S-0.0173 Å °0.0213 Å °0.0251 Å °-0.0152 Å °0.0143 Å °0.0142 Å °0.0094 Å °-0.0268 Å °0.003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA12 - 175
2X-RAY DIFFRACTION1A201

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