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- PDB-2vra: Drosophila Robo IG1-2 (monoclinic form) -

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Basic information

Entry
Database: PDB / ID: 2vra
TitleDrosophila Robo IG1-2 (monoclinic form)
ComponentsROUNDABOUT 1
KeywordsCELL ADHESION / IMMUNOGLOBULIN-LIKE DOMAIN / AXON GUIDANCE / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


Slit-Robo signaling complex / dendrite guidance / regulation of epithelial cell migration, open tracheal system / salivary gland boundary specification / photoreceptor cell axon guidance / neuron recognition / gonad development / axon guidance receptor activity / regulation of dendrite development / positive regulation of cell-cell adhesion ...Slit-Robo signaling complex / dendrite guidance / regulation of epithelial cell migration, open tracheal system / salivary gland boundary specification / photoreceptor cell axon guidance / neuron recognition / gonad development / axon guidance receptor activity / regulation of dendrite development / positive regulation of cell-cell adhesion / Roundabout signaling pathway / entrainment of circadian clock / embryonic heart tube development / motor neuron axon guidance / axon midline choice point recognition / dendrite morphogenesis / muscle cell cellular homeostasis / outflow tract morphogenesis / axonal growth cone / axon guidance / heparin binding / vesicle / cell adhesion / axon / neuronal cell body / dendrite / protein-containing complex / plasma membrane
Similarity search - Function
Roundabout homologue 1 / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. ...Roundabout homologue 1 / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFukuhara, N. / Howitt, J.A. / Hussain, S. / Hohenester, E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Functional Analysis of Slit and Heparin Binding to Immunoglobulin-Like Domains 1 and 2 of Drosophila Robo
Authors: Fukuhara, N. / Howitt, J.A. / Hussain, S. / Hohenester, E.
History
DepositionMar 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ROUNDABOUT 1
B: ROUNDABOUT 1
C: ROUNDABOUT 1
D: ROUNDABOUT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,60316
Polymers92,3744
Non-polymers2,23012
Water00
1
A: ROUNDABOUT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3824
Polymers23,0931
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ROUNDABOUT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4584
Polymers23,0931
Non-polymers1,3653
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ROUNDABOUT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3824
Polymers23,0931
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ROUNDABOUT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3824
Polymers23,0931
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.935, 84.430, 107.133
Angle α, β, γ (deg.)90.00, 98.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, -0.007, 0.016), (-0.009, -0.533, -0.846), (0.014, -0.846, 0.532)147.413, 109.345, 59.314
2given(0.812, -0.509, -0.287), (-0.505, -0.858, 0.093), (-0.294, 0.07, -0.953)49.701, 141.28, 66.539
3given(-0.819, 0.498, 0.286), (0.512, 0.406, 0.757), (0.261, 0.767, -0.587)99.09, -22.897, -23.491

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Components

#1: Protein
ROUNDABOUT 1 / ROBO


Mass: 23093.375 Da / Num. of mol.: 4 / Fragment: IG1-2, RESIDUES 51-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: O44924
#2: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1172.956 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY
Sequence detailsN-TERMINAL APLA IS VECTOR DERIVED

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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: 3.02 Å3/Da / Density % sol: 59 % / Description: SEARCH MODEL WAS ROBO IG1-2 TETRAGONAL FORM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.12
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 19035 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VR9

2vr9


Resolution: 3.2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1873 9.8 %RANDOM
Rwork0.2513 ---
obs0.2513 19024 99.5 %-
Solvent computationSolvent model: FLAT / Bsol: 29.0017 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.595 Å20 Å2-3.101 Å2
2--9.04 Å20 Å2
3---10.555 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 125 0 5939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.2862
X-RAY DIFFRACTIONc_scbond_it2.2742
X-RAY DIFFRACTIONc_scangle_it2.1162.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2HEPARIN.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM

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