[English] 日本語
Yorodumi
- PDB-3p1w: Crystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p1w
TitleCrystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c
ComponentsRabGDI protein
KeywordsPROTEIN TRANSPORT / GDI RAB / malaria / Structural Genomics Consortium / SGC / transport / PF10_0345
Function / homology
Function and homology information


RAB GEFs exchange GTP for GDP on RABs / Rab GDP-dissociation inhibitor activity / Neutrophil degranulation / small GTPase-mediated signal transduction / vesicle-mediated transport / GTPase activator activity / protein transport / cytosol
Similarity search - Function
Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rab GDP dissociation inhibitor
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsWernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / Pizzaro, J.C. / Hutchinson, A. / Structural Genomics Consortium (SGC)
Citation
Journal: To be published
Title: Crystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c
Authors: Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / ...Authors: Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / Pizzaro, J.C. / Hutchinson, A.
#1: Journal: Mol.Biochem.Parasitol. / Year: 1996
Title: A Plasmodium falciparum homologue of a rab specific GDP dissociation inhibitor.
Authors: Attal, G. / Langsley, G.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 29, 2014Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RabGDI protein


Theoretical massNumber of molelcules
Total (without water)54,3531
Polymers54,3531
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.885, 116.565, 125.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein RabGDI protein


Mass: 54353.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFL2060c / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I501
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.1 M Hepes 7.5, 0.2 M NaCl2, 2 mM TCEP, 5% MPD, glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 59119 / Num. obs: 57819 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.038 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.76-1.795.90.9891.5723710.85481.3
1.79-1.826.70.9241.8428540.91196.9
1.82-1.867.10.7142.5828380.90697.7
1.86-1.97.10.618328550.92698
1.9-1.947.10.53328680.98598.1
1.94-1.987.10.37628800.99398.3
1.98-2.037.20.30628931.00998.2
2.03-2.097.20.2528831.03898.5
2.09-2.157.20.20828901.06998.7
2.15-2.227.20.15729131.08298.9
2.22-2.37.20.13128821.11498.7
2.3-2.397.30.11429091.06498.9
2.39-2.57.30.09629211.06799.1
2.5-2.637.30.08229571.06999.3
2.63-2.797.40.06429041.03999.1
2.79-3.017.40.05129591.05599.4
3.01-3.317.40.04329461.19199.5
3.31-3.797.30.03729951.4799.6
3.79-4.787.10.02730191.08999.8
4.78-5070.02130820.71198.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.88 Å
Translation2.5 Å45.88 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LV0

1lv0


Resolution: 1.85→40.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8908 / SU B: 5.216 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1169 / SU Rfree: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 2571 5.1 %RANDOM
Rwork0.1804 ---
all0.1814 51043 --
obs0.1814 50360 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.78 Å2 / Biso mean: 34.569 Å2 / Biso min: 6.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---2.03 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 0 215 3738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223698
X-RAY DIFFRACTIONr_bond_other_d0.0020.022444
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9585039
X-RAY DIFFRACTIONr_angle_other_deg0.87236024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64925.427164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.808157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
X-RAY DIFFRACTIONr_mcbond_it0.6671.52256
X-RAY DIFFRACTIONr_mcbond_other0.181.5909
X-RAY DIFFRACTIONr_mcangle_it1.19523679
X-RAY DIFFRACTIONr_scbond_it1.79931442
X-RAY DIFFRACTIONr_scangle_it2.9044.51357
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 197 -
Rwork0.259 3439 -
all-3636 -
obs--97.82 %
Refinement TLS params.Method: refined / Origin x: 22.4039 Å / Origin y: 14.5863 Å / Origin z: 44.0026 Å
111213212223313233
T0.0697 Å20.0521 Å2-0.0073 Å2-0.0721 Å2-0.0064 Å2--0.0317 Å2
L1.5942 °2-0.5137 °2-0.1015 °2-1.495 °20.4588 °2--1.0229 °2
S0.1329 Å °0.3067 Å °-0.0218 Å °-0.1596 Å °-0.1369 Å °0.074 Å °-0.0253 Å °-0.049 Å °0.004 Å °

+
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