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- PDB-5o5g: Robo1 Ig1 to 4 crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5o5g
TitleRobo1 Ig1 to 4 crystal form 1
ComponentsRoundabout homolog 1
KeywordsSIGNALING PROTEIN / Neuronal receptor
Function / homology
Function and homology information


chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / axon guidance receptor activity / heart induction / positive regulation of vascular endothelial growth factor signaling pathway / Netrin-1 signaling ...chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / axon guidance receptor activity / heart induction / positive regulation of vascular endothelial growth factor signaling pathway / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / Role of ABL in ROBO-SLIT signaling / Inactivation of CDC42 and RAC1 / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / aortic valve morphogenesis / cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / Activation of RAC1 / axon midline choice point recognition / aorta development / positive regulation of Rho protein signal transduction / positive regulation of axonogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of cell migration / positive regulation of MAP kinase activity / Regulation of expression of SLITs and ROBOs / activation of cysteine-type endopeptidase activity involved in apoptotic process / nervous system development / cell adhesion / neuron projection / axon / negative regulation of gene expression / positive regulation of gene expression / cell surface / identical protein binding / plasma membrane / cytoplasm
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
Similarity search - Domain/homology
Roundabout homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsAleksandrova, N. / Gutsche, I. / Kandiah, E. / Avilov, S.V. / Petoukhov, M.V. / Seiradake, E. / McCarthy, A.A.
CitationJournal: Structure / Year: 2018
Title: Robo1 Forms a Compact Dimer-of-Dimers Assembly.
Authors: Aleksandrova, N. / Gutsche, I. / Kandiah, E. / Avilov, S.V. / Petoukhov, M.V. / Seiradake, E. / McCarthy, A.A.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
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 / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roundabout homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0492
Polymers42,8281
Non-polymers2211
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.156, 99.711, 238.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Roundabout homolog 1 / Deleted in U twenty twenty / H-Robo-1


Mass: 42828.227 Da / Num. of mol.: 1 / Fragment: UNP residues 63-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO1, DUTT1 / Plasmid: pTT3 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9Y6N7
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 6% PEG 4000, 100 mM Sodium citrate, 10 mM Calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2007 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 10679 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 63.1 Å2 / Rpim(I) all: 0.13 / Net I/σ(I): 6.4
Reflection shellResolution: 3→3.2 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1866 / CC1/2: 0.65 / Rpim(I) all: 0.447 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS1st March 2015data reduction
XSCALE1st March 2015data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v9r

2v9r


Resolution: 3.03→28.34 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.804 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.405
RfactorNum. reflection% reflectionSelection details
Rfree0.258 560 5.26 %RANDOM
Rwork0.198 ---
obs0.201 10652 99.7 %-
Displacement parametersBiso mean: 59.97 Å2
Baniso -1Baniso -2Baniso -3
1--7.3756 Å20 Å20 Å2
2--26.7711 Å20 Å2
3----19.3955 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 3.03→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 14 16 2918
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092967HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.154041HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1009SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes438HARMONIC5
X-RAY DIFFRACTIONt_it2967HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion19.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion400SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2993SEMIHARMONIC4
LS refinement shellResolution: 3.03→3.39 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2791 160 5.39 %
Rwork0.2358 2809 -
all0.238 2969 -
obs--99.73 %

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