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- PDB-2cxl: RUN domain of Rap2 interacting protein x, crystallized in I422 sp... -

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Basic information

Entry
Database: PDB / ID: 2cxl
TitleRUN domain of Rap2 interacting protein x, crystallized in I422 space group
Componentsrap2 interacting protein x
KeywordsPROTEIN BINDING / RUN domain / helix bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of axonogenesis / positive regulation of intracellular protein transport / anchoring junction / regulation of establishment of cell polarity / positive regulation of axonogenesis / regulation of axonogenesis / endomembrane system / positive regulation of axon extension / filopodium / actin filament organization ...negative regulation of axonogenesis / positive regulation of intracellular protein transport / anchoring junction / regulation of establishment of cell polarity / positive regulation of axonogenesis / regulation of axonogenesis / endomembrane system / positive regulation of axon extension / filopodium / actin filament organization / lamellipodium / nervous system development / growth cone / perikaryon / cell differentiation / positive regulation of cell migration / axon / neuronal cell body / dendrite / membrane / cytoplasm
Similarity search - Function
: / : / RUN domain / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKukimoto-Niino, M. / Umehara, T. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the RUN Domain of the RAP2-interacting Protein x
Authors: Kukimoto-Niino, M. / Takagi, T. / Akasaka, R. / Murayama, K. / Uchikubo-Kamo, T. / Terada, T. / Inoue, M. / Watanabe, S. / Tanaka, A. / Hayashizaki, Y. / Kigawa, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rap2 interacting protein x


Theoretical massNumber of molelcules
Total (without water)21,4451
Polymers21,4451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.774, 112.774, 76.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein rap2 interacting protein x


Mass: 21445.293 Da / Num. of mol.: 1 / Fragment: RUN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Plasmid: PX040220-04-MD01 / References: UniProt: Q9D394

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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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.6
Details: PEG4000, Lithium Sulfate, Tris-HCl, pH 7.6, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97888, 0.97951, 0.97600, 0.98300
DetectorDetector: CCD / Date: May 16, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.979511
30.9761
40.9831
ReflectionResolution: 3.18→50 Å / Num. obs: 4293 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.0547 % / Rsym value: 0.11 / Net I/σ(I): 15.2776
Reflection shellResolution: 3.18→3.29 Å / Mean I/σ(I) obs: 5.51505 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WUS

1wus
PDB Unreleased entry


Resolution: 3.2→42.1 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 111601.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.36 444 10.3 %RANDOM
Rwork0.28 ---
obs0.28 4291 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 123.806 Å2 / ksol: 0.407703 e/Å3
Displacement parametersBiso mean: 52.1 Å2
Baniso -1Baniso -2Baniso -3
1-14.83 Å20 Å20 Å2
2--14.83 Å20 Å2
3----29.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3.2→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 0 0 1230
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.55
LS refinement shellResolution: 3.18→3.38 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.446 63 10.1 %
Rwork0.319 559 -
obs--88.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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