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- PDB-6igt: MPZL1 mutant - V145G, Q146K, P147T and G148S -

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Basic information

Entry
Database: PDB / ID: 6igt
TitleMPZL1 mutant - V145G, Q146K, P147T and G148S
ComponentsMyelin protein zero-like protein 1
KeywordsMEMBRANE PROTEIN / receptor / glycoprotein / transmembrane / immunoglobulin
Function / homology
Function and homology information


cell surface receptor protein tyrosine kinase signaling pathway / cell-cell signaling / focal adhesion / structural molecule activity / cell surface / plasma membrane
Similarity search - Function
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 ...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
Myelin protein zero-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsYu, T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural and biochemical studies of the extracellular domain of Myelin protein zero-like protein 1
Authors: Yu, T. / Liang, L. / Zhao, X. / Yin, Y.
History
DepositionSep 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myelin protein zero-like protein 1
B: Myelin protein zero-like protein 1
C: Myelin protein zero-like protein 1
D: Myelin protein zero-like protein 1


Theoretical massNumber of molelcules
Total (without water)60,8524
Polymers60,8524
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-10 kcal/mol
Surface area23640 Å2
Unit cell
Length a, b, c (Å)40.425, 40.417, 195.223
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Myelin protein zero-like protein 1 / / Protein zero-related


Mass: 15212.998 Da / Num. of mol.: 4 / Fragment: UNP residues 36-162 / Mutation: V145G,Q146K,P147T,G148S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPZL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95297

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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: 2.62 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 50mM MES pH5.6, 100 mM (NH4)2SO4, 10mM MgCl2, 20% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23051 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rpim(I) all: 0.046 / Net I/σ(I): 14.89
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 1330 / Rpim(I) all: 0.349

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Processing

Software
NameVersionClassification
PHENIX(dev_2400: ???)refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OAI

3oai


Resolution: 2.404→40.425 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.47
RfactorNum. reflection% reflection
Rfree0.2515 1184 5.14 %
Rwork0.2203 --
obs0.2219 23043 91.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.404→40.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 0 0 0 3690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093780
X-RAY DIFFRACTIONf_angle_d1.1435108
X-RAY DIFFRACTIONf_dihedral_angle_d22.4561352
X-RAY DIFFRACTIONf_chiral_restr0.234550
X-RAY DIFFRACTIONf_plane_restr0.006648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4042-2.51360.3786940.31391660X-RAY DIFFRACTION56
2.5136-2.64610.34371460.30212486X-RAY DIFFRACTION86
2.6461-2.81180.29281660.27082863X-RAY DIFFRACTION98
2.8118-3.02890.28281670.24692942X-RAY DIFFRACTION99
3.0289-3.33350.25561760.23082936X-RAY DIFFRACTION99
3.3335-3.81560.25291300.21282936X-RAY DIFFRACTION99
3.8156-4.8060.18931370.18172996X-RAY DIFFRACTION99
4.806-40.43030.2251680.2033040X-RAY DIFFRACTION98

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