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- PDB-4ykd: Crystal structure of truncated cerebral cavernous malformation 2 ... -

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Basic information

Entry
Database: PDB / ID: 4ykd
TitleCrystal structure of truncated 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 / MOLECULAR REPLACEMENT / Resolution: 1.932 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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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)11,3031
Polymers11,3031
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5240 Å2
Unit cell
Length a, b, c (Å)51.360, 51.360, 137.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Malcavernin / Cerebral cavernous malformations 2 protein


Mass: 11302.810 Da / Num. of mol.: 1
Fragment: truncated fragment of C-terminal adaptor domain, UNP residues 290-376
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 550, 50 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97908 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.93→37.31 Å / Num. obs: 8320 / % possible obs: 97.3 % / Redundancy: 21.1 % / Biso Wilson estimate: 24.04 Å2 / Rsym value: 0.042 / Net I/σ(I): 55.5
Reflection shellResolution: 1.93→2.04 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 30.5 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YKC

4ykc


Resolution: 1.932→31.864 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 392 4.71 %Random
Rwork0.2004 ---
obs0.2021 8320 96.23 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.609 Å2 / ksol: 0.407 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5608 Å20 Å2-0 Å2
2--0.5608 Å20 Å2
3----1.1217 Å2
Refinement stepCycle: LAST / Resolution: 1.932→31.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms688 0 0 74 762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014701
X-RAY DIFFRACTIONf_angle_d1.406943
X-RAY DIFFRACTIONf_dihedral_angle_d14.792263
X-RAY DIFFRACTIONf_chiral_restr0.087104
X-RAY DIFFRACTIONf_plane_restr0.007122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.932-2.21150.29531310.21772540X-RAY DIFFRACTION96
2.2115-2.78610.27661270.19632616X-RAY DIFFRACTION97
2.7861-31.86850.20171340.19782772X-RAY DIFFRACTION96

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