[English] 日本語
Yorodumi
- PDB-2ca6: MIRAS structure determination from hemihedrally twinned crystals -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ca6
TitleMIRAS structure determination from hemihedrally twinned crystals
ComponentsRAN GTPASE-ACTIVATING PROTEIN 1
KeywordsSIGNALING REGULATOR / GAP / GTPASE ACTIVATION / GTPASE-ACTIVATING PROTEIN / HEMIHEDRAL TWINNING / LEUCINE-RICH REPEAT PROTEIN / LRR / MEROHEDRAL TWINNING / MEROHEDRY / RANGAP / RNA1P / SIGNALING PROTEIN / SIGNALING ACTIVATOR / NUCLEAR TRANSPORT
Function / homology
Function and homology information


SUMOylation of nuclear envelope proteins / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / small GTPase-mediated signal transduction / nuclear periphery / GTPase activator activity / positive regulation of protein export from nucleus / small GTPase binding / perinuclear region of cytoplasm / nucleus ...SUMOylation of nuclear envelope proteins / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / small GTPase-mediated signal transduction / nuclear periphery / GTPase activator activity / positive regulation of protein export from nucleus / small GTPase binding / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Leucine rich repeat, ribonuclease inhibitor type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsHillig, R.C. / Renault, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Detecting and Overcoming Hemihedral Twinning During the Mir Structure Determination of RNA1P.
Authors: Hillig, R.C. / Renault, L.
#1: Journal: Mol.Cell / Year: 1999
Title: The Crystal Structure of RNA1P: A New Fold for a Gtpase-Activating Protein
Authors: Hillig, R.C. / Renault, L. / Vetter, I.R. / Drell, T. / Wittinghofer, A. / Becker, J.
#2: Journal: Nature / Year: 2002
Title: Rangap Mediates GTP Hydrolysis without an Arginine Finger
Authors: Seewald, M.J. / Korner, C. / Wittinghofer, A. / Vetter, I.R.
History
DepositionDec 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAN GTPASE-ACTIVATING PROTEIN 1
B: RAN GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9306
Polymers86,5452
Non-polymers3844
Water4,918273
1
A: RAN GTPASE-ACTIVATING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)43,2731
Polymers43,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RAN GTPASE-ACTIVATING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6575
Polymers43,2731
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)175.210, 175.210, 55.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99729, 0.07335, 0.00611), (0.07336, 0.9973, 0.00167), (-0.00597, 0.00211, -0.99998)
Vector: 76.84581, -3.71842, 47.88696)

-
Components

#1: Protein RAN GTPASE-ACTIVATING PROTEIN 1 / RNA1P / PROTEIN RNA1


Mass: 43272.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-TERMINI OF BOTH COPIES OF RNA1P (RESIDUES 345-386) ARE DISORDERED AND WERE OMITTED FROM THE MODEL
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P41391
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGTPASE ACTIVATOR FOR THE NUCLEAR RAS-RELATED REGULATORY PROTEIN SPI1 (RAN), CONVERTING IT TO THE ...GTPASE ACTIVATOR FOR THE NUCLEAR RAS-RELATED REGULATORY PROTEIN SPI1 (RAN), CONVERTING IT TO THE GDP-BOUND STATE.
Sequence detailsTHE CONFLICT SHOWN IN THE SEQADV RECORDS BELOW SER2ALA IS A CLONING ARTEFACT DUE TO EXPRESSION ...THE CONFLICT SHOWN IN THE SEQADV RECORDS BELOW SER2ALA IS A CLONING ARTEFACT DUE TO EXPRESSION SYSTEM. MET 1 IS CLEAVED OFF.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 55.4 %
Crystal growpH: 8.5
Details: 2 MICROLITER PROTEIN (25MG/ML IN 20MM TRIS-HCL PH7.5, 2MMDTE) AND 2 MICROLITER RESERVOIR (24% PEG2000MME, 100MM TRIS PH8.5, 200MM LI2SO4, 20MM MGCL2)., pH 8.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0093
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.2→31 Å / Num. obs: 42106 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.14 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.37 / % possible all: 87.4

-
Processing

Software
NameVersionClassification
CNX2002refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→31 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE DATA SET SHOWS HEMIHEDRAL TWINNING WITH A HIGH TWIN FRACTION OF 0.39. THE MODEL WAS REFINED AGAINST THIS ORIGINAL DATA SET, I.E. REFLECTIONS NOT TWIN CORRECTED, BY USING CNX IN TWIN MODE. ...Details: THE DATA SET SHOWS HEMIHEDRAL TWINNING WITH A HIGH TWIN FRACTION OF 0.39. THE MODEL WAS REFINED AGAINST THIS ORIGINAL DATA SET, I.E. REFLECTIONS NOT TWIN CORRECTED, BY USING CNX IN TWIN MODE. ALL R FACTORS ARE SO CALLED TWINNED R FACTORS, CALCULATED FROM THE DIFFERENCES BETWEEN THE ORIGINAL TWINNED REFLECTIONS AND THE ARTIFICIALLY TWINNED REFLECTIONS CALCULATED FROM THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 3957 9.1 %CNX SCRIPT MAKE_CV_ TWIN.INP, ENSURES THAT TWIN -RELATED PAIRS OF REFLECTIONS ARE EITHER BOTH IN TEST OR BOTH IN WORK SET
Rwork0.1651 ---
obs-41215 --
Solvent computationSolvent model: MASK AROUND THE MOLECULE, DETERMINED AUTOMATICALLY BY CNX
Bsol: 38.2404 Å2 / ksol: 0.352164 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.948 Å20 Å20 Å2
2---3.948 Å20 Å2
3---7.896 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 20 273 5673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.8972
X-RAY DIFFRACTIONc_mcangle_it2.7753
X-RAY DIFFRACTIONc_scbond_it5.3174.5
X-RAY DIFFRACTIONc_scangle_it6.4596
LS refinement shellResolution: 2.2→2.24 Å / Total num. of bins used: 20 /
Rfactor% reflection
Rfree0.277 -
Rwork0.231 -
obs-76.25 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: ION.TOP

+
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