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- PDB-3oai: Crystal structure of the extra-cellular domain of human myelin pr... -

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Basic information

Entry
Database: PDB / ID: 3oai
TitleCrystal structure of the extra-cellular domain of human myelin protein zero
ComponentsMaltose-binding periplasmic protein, Myelin protein P0
KeywordsMEMBRANE PROTEIN / CELL ADHESION / Schwann cell membrane protein / Immunoglobulin-folding / intercelluar adhesion / tetramer
Function / homology
Function and homology information


cell aggregation / cell-cell adhesion via plasma-membrane adhesion molecules / EGR2 and SOX10-mediated initiation of Schwann cell myelination / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport ...cell aggregation / cell-cell adhesion via plasma-membrane adhesion molecules / EGR2 and SOX10-mediated initiation of Schwann cell myelination / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / myelination / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / myelin sheath / outer membrane-bounded periplasmic space / chemical synaptic transmission / periplasmic space / synapse / DNA damage response / structural molecule activity / membrane / plasma membrane
Similarity search - Function
: / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein ...: / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / Myelin protein P0
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, Z. / Wang, Y. / Brunzelle, J. / Kovari, I.A. / Sohi, J. / Kamholz, J. / Kovari, L.C.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of the extracellular domain of human myelin protein zero.
Authors: Liu, Z. / Wang, Y. / Yedidi, R.S. / Brunzelle, J.S. / Kovari, I.A. / Sohi, J. / Kamholz, J. / Kovari, L.C.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Myelin protein P0
B: Maltose-binding periplasmic protein, Myelin protein P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4164
Polymers112,7322
Non-polymers6852
Water9,080504
1
A: Maltose-binding periplasmic protein, Myelin protein P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7082
Polymers56,3661
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein, Myelin protein P0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7082
Polymers56,3661
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.900, 54.886, 146.069
Angle α, β, γ (deg.)90.00, 98.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltose-binding periplasmic protein, Myelin protein P0


Mass: 56365.797 Da / Num. of mol.: 2
Fragment: UNP D3QK41_ECOCB residues 27-392, UNP MYP0_HUMAN residues 30-150)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
References: UniProt: D3QK41, UniProt: P25189, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 11.1
Details: 40% PEG 8000, 0.1 M KSCN, 0.1 M Tris, pH 11.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9779 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 77053 / Num. obs: 77053 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.087
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.071100
2.07-2.151100
2.15-2.251100
2.25-2.371100
2.37-2.52199.9
2.52-2.71199.7
2.71-2.99199.8
2.99-3.42199.7
3.42-4.31199.7
4.31-30199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.463 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25227 2895 5.1 %RANDOM
Rwork0.18296 ---
all0.18643 77053 --
obs0.18643 53992 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.189 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7662 0 46 504 8212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.95510752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9965972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73825.419358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.653151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.961520
X-RAY DIFFRACTIONr_chiral_restr0.1440.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1161.54852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9627812
X-RAY DIFFRACTIONr_scbond_it3.10833056
X-RAY DIFFRACTIONr_scangle_it4.8364.52940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 193 -
Rwork0.215 3919 -
all-4112 -
obs--99.9 %

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