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- PDB-5l74: Plexin A2 extracellular segment domains 4-5 (PSI2-IPT2), resoluti... -

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Basic information

Entry
Database: PDB / ID: 5l74
TitlePlexin A2 extracellular segment domains 4-5 (PSI2-IPT2), resolution 1.36 Angstrom
ComponentsPlexin-A2
KeywordsSIGNALING PROTEIN / receptor / axon guidance / PSI-IPT domains
Function / homology
Function and homology information


cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / limb bud formation / pharyngeal system development / semaphorin receptor activity / neural tube development / centrosome localization / semaphorin-plexin signaling pathway ...cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / limb bud formation / pharyngeal system development / semaphorin receptor activity / neural tube development / centrosome localization / semaphorin-plexin signaling pathway / somitogenesis / regulation of cell migration / : / cell surface receptor signaling pathway / identical protein binding / plasma membrane
Similarity search - Function
Plexin-A2, sema domain / Plexin A/B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain ...Plexin-A2, sema domain / Plexin A/B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKong, Y. / Janssen, B.J.C. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J.C. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKA10976 United Kingdom
Medical Research Council (United Kingdom)G9900061 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Neuron / Year: 2016
Title: Structural Basis for Plexin Activation and Regulation.
Authors: Kong, Y. / Janssen, B.J. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y.
History
DepositionJun 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Plexin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6507
Polymers16,9051
Non-polymers7456
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-30 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.710, 44.560, 33.010
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Plexin-A2 / Plexin-2


Mass: 16905.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna2, Kiaa0463 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P70207
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) polyethylene glycol 3,350 and 100 mM BIS-TRIS pH 5.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0163 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0163 Å / Relative weight: 1
ReflectionResolution: 1.36→52.1 Å / Num. obs: 27859 / % possible obs: 85.6 % / Redundancy: 3.7 % / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→52.092 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.79
RfactorNum. reflection% reflection
Rfree0.2025 1400 5.03 %
Rwork0.1745 --
obs0.1759 27856 85.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.36→52.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 45 97 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121279
X-RAY DIFFRACTIONf_angle_d1.2981755
X-RAY DIFFRACTIONf_dihedral_angle_d19.7490
X-RAY DIFFRACTIONf_chiral_restr0.105201
X-RAY DIFFRACTIONf_plane_restr0.008230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3601-1.40870.2309610.24991302X-RAY DIFFRACTION43
1.4087-1.46510.23771010.20791773X-RAY DIFFRACTION57
1.4651-1.53180.21721360.19392527X-RAY DIFFRACTION82
1.5318-1.61250.21161510.1842888X-RAY DIFFRACTION95
1.6125-1.71360.21021650.18162945X-RAY DIFFRACTION95
1.7136-1.84590.19841420.18172957X-RAY DIFFRACTION95
1.8459-2.03170.21051650.1692974X-RAY DIFFRACTION97
2.0317-2.32570.21351620.17143010X-RAY DIFFRACTION97
2.3257-2.93010.22591620.18173040X-RAY DIFFRACTION97
2.9301-52.13040.17541550.16253040X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24390.10570.20420.7523-0.08520.84940.0089-0.07180.02640.26350.0504-0.165-0.02810.13250.00890.16280.0273-0.00620.1406-0.00560.113436.6585.735522.4117
21.3743-0.46690.48481.2294-0.17261.21850.01690.1391-0.04640.0394-0.01920.18230.0757-0.01610.00430.0985-0.00020.02810.10210.00940.111820.02853.34884.9054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 653 through 700 )
2X-RAY DIFFRACTION2chain 'A' and (resid 701 through 803 )

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