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- PDB-4ykc: Crystal structure of cerebral cavernous malformation 2 C-terminal... -

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Basic information

Entry
Database: PDB / ID: 4ykc
TitleCrystal structure of cerebral cavernous malformation 2 C-terminal adaptor domain
ComponentsMalcavernin
KeywordsPROTEIN BINDING / adaptor protein
Function / homology
Function and homology information


endothelial cell development / venous blood vessel morphogenesis / blood vessel endothelial cell differentiation / pericardium development / endothelium development / endothelial tube morphogenesis / cell-cell junction organization / inner ear development / vasculogenesis / regulation of angiogenesis ...endothelial cell development / venous blood vessel morphogenesis / blood vessel endothelial cell differentiation / pericardium development / endothelium development / endothelial tube morphogenesis / cell-cell junction organization / inner ear development / vasculogenesis / regulation of angiogenesis / stress-activated MAPK cascade / integrin-mediated signaling pathway / multicellular organism growth / heart development / in utero embryonic development / protein-containing complex / mitochondrion / cytoplasm
Similarity search - Function
Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / Paired amphipathic helix 2 (pah2 repeat) - #20 / Paired amphipathic helix 2 (pah2 repeat) / Phosphotyrosine interaction domain (PID) profile. / PTB/PI domain / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cerebral cavernous malformations 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsDing, J. / Wang, X. / Wang, D.C.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Ministry of Science and Technology 973 program2011CB910304 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08020200 China
CitationJournal: Structure / Year: 2015
Title: Structural Insights into the Molecular Recognition between Cerebral Cavernous Malformation 2 and Mitogen-Activated Protein Kinase Kinase Kinase 3
Authors: Wang, X. / Hou, Y. / Deng, K. / Zhang, Y. / Wang, D.C. / Ding, J.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malcavernin


Theoretical massNumber of molelcules
Total (without water)18,6771
Polymers18,6771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6510 Å2
Unit cell
Length a, b, c (Å)113.300, 113.300, 102.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Malcavernin / Cerebral cavernous malformations 2 protein


Mass: 18676.973 Da / Num. of mol.: 1 / Fragment: C-terminal adaptor domain, UNP residues 290-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCM2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BSQ5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 72.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 45% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.7→45.41 Å / Num. all: 9435 / Num. obs: 9435 / % possible obs: 99.7 % / Redundancy: 14.3 % / Biso Wilson estimate: 62.77 Å2 / Rsym value: 0.077 / Net I/σ(I): 23.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→43.187 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 451 4.79 %Random
Rwork0.219 ---
obs0.2212 9422 99.6 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.347 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5078 Å2-0 Å20 Å2
2---3.5078 Å2-0 Å2
3---7.0157 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 0 0 844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004858
X-RAY DIFFRACTIONf_angle_d0.7011153
X-RAY DIFFRACTIONf_dihedral_angle_d14.8321
X-RAY DIFFRACTIONf_chiral_restr0.045128
X-RAY DIFFRACTIONf_plane_restr0.002148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-3.09070.35711580.29612923X-RAY DIFFRACTION100
3.0907-3.89350.23941470.21522968X-RAY DIFFRACTION100
3.8935-43.19270.25861460.20363080X-RAY DIFFRACTION99

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