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- PDB-1iko: CRYSTAL STRUCTURE OF THE MURINE EPHRIN-B2 ECTODOMAIN -

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Basic information

Entry
Database: PDB / ID: 1iko
TitleCRYSTAL STRUCTURE OF THE MURINE EPHRIN-B2 ECTODOMAIN
ComponentsEPHRIN-B2Ephrin B2
KeywordsSIGNALING PROTEIN / GREEK KEY / GLYCOSYLATION
Function / homology
Function and homology information


Ephrin signaling / EPH-Ephrin signaling / EPH-ephrin mediated repulsion of cells / venous blood vessel morphogenesis / EPHB-mediated forward signaling / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development ...Ephrin signaling / EPH-Ephrin signaling / EPH-ephrin mediated repulsion of cells / venous blood vessel morphogenesis / EPHB-mediated forward signaling / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development / regulation of chemotaxis / cell migration involved in sprouting angiogenesis / regulation of postsynaptic neurotransmitter receptor internalization / adherens junction organization / blood vessel morphogenesis / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / T cell costimulation / ephrin receptor binding / axon guidance / postsynaptic density membrane / adherens junction / animal organ morphogenesis / Schaffer collateral - CA1 synapse / negative regulation of neuron projection development / presynaptic membrane / cell adhesion / signaling receptor binding / dendrite / glutamatergic synapse / positive regulation of cell population proliferation / plasma membrane
Similarity search - Function
Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.92 Å
AuthorsToth, J. / Cutforth, T. / Gelinas, A.D. / Bethoney, K.A. / Bard, J. / Harrison, C.J.
CitationJournal: Dev.Cell / Year: 2001
Title: Crystal structure of an ephrin ectodomain.
Authors: Toth, J. / Cutforth, T. / Gelinas, A.D. / Bethoney, K.A. / Bard, J. / Harrison, C.J.
History
DepositionMay 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE SOME AMBIGUITY IN THE EXACT C-TERMINUS SEQUENCE EXISTS DUE TO A GLU-C DIGEST.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: EPHRIN-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4852
Polymers19,8981
Non-polymers5871
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.283, 59.283, 168.868
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11P-293-

HOH

21P-299-

HOH

31P-326-

HOH

41P-395-

HOH

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Components

#1: Protein EPHRIN-B2 / Ephrin B2 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5 / LERK-5 / HTK LIGAND / HTK-L / ELF-2


Mass: 19898.439 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 30-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ephrin-B2 / Plasmid: PIC-Zalpha / Production host: Pichia pastoris (fungus) / References: UniProt: P52800
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: magnesium chloride, PEG 4000, trishydroxyethylmethane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130-98 mg/mlprotein1drop
2100 mMTris1reservoirpH8.5
3200 mM1reservoirMgCl2
420 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 2, 2000 / Details: double mirrors
RadiationMonochromator: Two Rosenbaum-Rock monochromators double crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.92→19.41 Å / Num. all: 13862 / Num. obs: 13862 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.042 / Net I/σ(I): 48
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 10 % / Mean I/σ(I) obs: 18 / Rsym value: 0.219 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 19.5 Å / Num. obs: 14283 / Num. measured all: 315392 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.219

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.92→19.41 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1410 -random
Rwork0.216 ---
obs0.216 13862 97.7 %-
all-14067 --
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å22.93 Å20 Å2
2--3.32 Å20 Å2
3----6.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.92→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 39 201 1360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.92→1.99 Å / Total num. of bins used: 28
RfactorNum. reflection% reflection
Rfree0.2925 37 7.69 %
Rwork0.2487 399 -
obs--90.64 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.215 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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