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- PDB-2ca6: MIRAS structure determination from hemihedrally twinned crystals -

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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 / nuclear export / nuclear periphery / GTPase activator activity / protein export from nucleus / small GTPase binding / perinuclear region of cytoplasm / nucleus / cytoplasm / cytosol
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
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)

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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


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

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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: 2.48 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

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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

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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

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