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- PDB-2cxf: RUN domain of Rap2 interacting protein x, crystallized in C2 spac... -

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Basic information

Entry
Database: PDB / ID: 2cxf
TitleRUN domain of Rap2 interacting protein x, crystallized in C2 space group
Componentsrap2 interacting protein x
KeywordsPROTEIN BINDING / 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 / dendrite / neuronal cell body / membrane / cytosol / 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 / MAD / Resolution: 3.07 Å
AuthorsKukimoto-Niino, M. / 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 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.619, 41.592, 62.132
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number5
Space group name H-MC121

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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 / 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: 2.508365 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG20000, Bicine, Dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97899, 0.97935, 0.96400
DetectorDetector: CCD / Date: Oct 3, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979351
30.9641
ReflectionResolution: 3→50 Å / Num. obs: 3507 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4069 % / Rsym value: 0.089 / Net I/σ(I): 9.07169
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 6.35079 / Rsym value: 0.13 / % possible all: 63.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.07→14.99 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1292738.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 324 9.8 %RANDOM
Rwork0.237 ---
obs0.237 3294 80.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.5132 Å2 / ksol: 0.271508 e/Å3
Displacement parametersBiso mean: 99.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.09 Å20 Å243.38 Å2
2---43.45 Å20 Å2
3---51.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 3.07→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 0 0 1301
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.6
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d0.49
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.093 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 15 9.6 %
Rwork0.331 141 -
obs--22 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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