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- PDB-6igo: Crystal structure of myelin protein zero-like protein 1 (MPZL1) -

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Basic information

Entry
Database: PDB / ID: 6igo
TitleCrystal structure of myelin protein zero-like protein 1 (MPZL1)
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: 2.746 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 25, 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 1.2Dec 12, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,3206
Polymers91,3206
Non-polymers00
Water0
1
C: Myelin protein zero-like protein 1
A: Myelin protein zero-like protein 1


Theoretical massNumber of molelcules
Total (without water)30,4402
Polymers30,4402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-11 kcal/mol
Surface area11420 Å2
MethodPISA
2
B: Myelin protein zero-like protein 1
D: Myelin protein zero-like protein 1


Theoretical massNumber of molelcules
Total (without water)30,4402
Polymers30,4402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area11310 Å2
MethodPISA
3
E: Myelin protein zero-like protein 1

F: Myelin protein zero-like protein 1


Theoretical massNumber of molelcules
Total (without water)30,4402
Polymers30,4402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2100 Å2
ΔGint-12 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.462, 121.703, 70.395
Angle α, β, γ (deg.)90.00, 100.24, 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: 15220.012 Da / Num. of mol.: 6 / Fragment: UNP residues 36-162
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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 100mM Tris-HCl pH 8.5, 1.15M (NH4)2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.746→50 Å / Num. obs: 22192 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rpim(I) all: 0.056 / Net I/σ(I): 11.87
Reflection shellResolution: 2.746→2.85 Å / Num. unique obs: 1700 / Rpim(I) all: 0.373

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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: 2.746→48.291 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.71
RfactorNum. reflection% reflection
Rfree0.2647 1047 4.72 %
Rwork0.2248 --
obs0.2267 22169 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.746→48.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 0 0 5666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015826
X-RAY DIFFRACTIONf_angle_d1.0947922
X-RAY DIFFRACTIONf_dihedral_angle_d22.0582094
X-RAY DIFFRACTIONf_chiral_restr0.06860
X-RAY DIFFRACTIONf_plane_restr0.0071016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7465-2.89130.33151170.27422432X-RAY DIFFRACTION78
2.8913-3.07240.34881400.28353047X-RAY DIFFRACTION96
3.0724-3.30950.27791510.26343109X-RAY DIFFRACTION99
3.3095-3.64250.31131600.24513136X-RAY DIFFRACTION100
3.6425-4.16930.27231550.22013157X-RAY DIFFRACTION100
4.1693-5.25190.22991610.18133120X-RAY DIFFRACTION100
5.2519-48.29890.21991630.20913121X-RAY DIFFRACTION97

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