[English] 日本語
Yorodumi
- PDB-6l6o: Crystal structure of stabilized Rab5a GTPase domain from Leishman... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 Rab domain profile. / Small GTPase Rho 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 ...: / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / Small GTPase Rab domain profile. / Small GTPase Rho 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-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


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


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


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more