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- PDB-1neu: STRUCTURE OF MYELIN MEMBRANE ADHESION MOLECULE P0 -

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Basic information

Entry
Database: PDB / ID: 1neu
TitleSTRUCTURE OF MYELIN MEMBRANE ADHESION MOLECULE P0
ComponentsMYELIN P0 PROTEIN
KeywordsSTRUCTURAL PROTEIN / MYELIN / GLYCOPROTEIN / TRANSMEMBRANE / PHOSPHORYLATION / IMMUNOGLOBULIN FOLD / MYELIN MEMBRANE ADHESION MOLECULE
Function / homology
Function and homology information


cell aggregation / cell-cell junction maintenance / cell-cell adhesion via plasma-membrane adhesion molecules / plasma membrane => GO:0005886 / rough endoplasmic reticulum / myelination / myelin sheath / basolateral plasma membrane / lysosome / negative regulation of apoptotic process / plasma membrane
Similarity search - Function
Myelin protein P0 / Myelin protein P0, C-terminal / Myelin P0 protein, conserved site / Myelin-PO cytoplasmic C-term p65 binding region / Myelin P0 protein signature. / Myelin P0 protein-related / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Myelin protein P0 / Myelin protein P0, C-terminal / Myelin P0 protein, conserved site / Myelin-PO cytoplasmic C-term p65 binding region / Myelin P0 protein signature. / Myelin P0 protein-related / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD, SIR/AS / Resolution: 1.9 Å
AuthorsShapiro, L. / Doyle, J.P. / Hensley, P. / Colman, D.R. / Hendrickson, W.A.
CitationJournal: Neuron / Year: 1996
Title: Crystal structure of the extracellular domain from P0, the major structural protein of peripheral nerve myelin.
Authors: Shapiro, L. / Doyle, J.P. / Hensley, P. / Colman, D.R. / Hendrickson, W.A.
History
DepositionSep 24, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYELIN P0 PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,1601
Polymers14,1601
Non-polymers00
Water2,954164
1
A: MYELIN P0 PROTEIN

A: MYELIN P0 PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,3192
Polymers28,3192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
Unit cell
Length a, b, c (Å)88.900, 88.900, 91.600
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 MYELIN P0 PROTEIN


Mass: 14159.656 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1 - 124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P06907
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.19 Å3/Da / Density % sol: 61.49 %
Description: PHASING WAS OBTAINED FROM A MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD) EXPERIMENT ON A PCMBS-DERIVATIZED CRYSTAL; THE MERCURY POSITION WAS POORLY OCCUPIED (~0.2), AND SO THE DERIVED ...Description: PHASING WAS OBTAINED FROM A MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD) EXPERIMENT ON A PCMBS-DERIVATIZED CRYSTAL; THE MERCURY POSITION WAS POORLY OCCUPIED (~0.2), AND SO THE DERIVED PHASES WERE COMBINED WITH PHASES OBTAINED BY SIR/AS ON A MORE COMPLETELY DERIVATIZED CRYSTAL.
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
145 mg/mlprotein1drop
210 mMTris1drop
30.3 M1dropNaCl
410 mMTris1reservoir
51.0 M1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 14552 / % possible obs: 98.2 % / Rmerge(I) obs: 0.041

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: MAD, SIR/AS / Resolution: 1.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.268 -5 %
Rwork0.215 --
obs0.215 14237 97.7 %
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 0 165 1096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.541
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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