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- PDB-5ope: Robo1 Ig1-4 crystals form 2 -

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Basic information

Entry
Database: PDB / ID: 5ope
TitleRobo1 Ig1-4 crystals form 2
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 / heart induction / axon guidance receptor activity / Netrin-1 signaling / positive regulation of vascular endothelial growth factor signaling pathway ...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 / heart induction / axon guidance receptor activity / Netrin-1 signaling / positive regulation of vascular endothelial growth factor signaling pathway / Role of ABL in ROBO-SLIT signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / Inactivation of CDC42 and RAC1 / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / aortic valve morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / axon midline choice point recognition / Activation of RAC1 / aorta development / positive regulation of axonogenesis / positive regulation of Rho protein signal transduction / 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 / synapse organization / 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 / neuronal cell body / 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
PHOSPHATE ION / Roundabout homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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
DepositionAug 9, 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 / Category: reflns_shell
Item: _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _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)42,9812
Polymers42,8861
Non-polymers951
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-4 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.457, 99.134, 247.175
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: 42886.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO1, DUTT1 / Plasmid: pTT3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y6N7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.11 Å3/Da / Density % sol: 60.5 % / Description: Plate like morphology
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.5 M ammonium phosphate, 100 mM Na Critrate

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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 13, 2007 / Details: Toroidal mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 17779 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.095 / Net I/σ(I): 4.9 / Num. measured all: 61677
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1772 / CC1/2: 0.53 / Rpim(I) all: 0.58 / % possible all: 82.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSOct 2015data reduction
Aimless1.9.31data scaling
PHASER2.5.7phasing
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o5g

5o5g


Resolution: 2.54→28.76 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.794 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.282 / SU Rfree Cruickshank DPI: 0.277
RfactorNum. reflection% reflectionSelection details
Rfree0.271 897 5.06 %RANDOM
Rwork0.212 ---
obs0.215 17735 97.8 %-
Displacement parametersBiso mean: 56.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.0034 Å20 Å20 Å2
2--11.5677 Å20 Å2
3----23.5711 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.54→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 5 133 2302
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092772HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153799HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d883SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it2772HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion19.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion393SEMIHARMONIC5
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_contact2800SEMIHARMONIC4
LS refinement shellResolution: 2.54→2.7 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3177 124 4.96 %
Rwork0.2489 2375 -
all0.2524 2499 -
obs--86.71 %
Refinement TLS params.Method: refined / Origin x: -14.938 Å / Origin y: 0.1155 Å / Origin z: 43.6112 Å
111213212223313233
T0.1453 Å20.0405 Å2-0.2102 Å2--0.1076 Å2-0.055 Å2---0.0516 Å2
L0.0727 °2-0.2707 °2-0.0554 °2-1.256 °20.2982 °2--0.4188 °2
S0.0807 Å °0.0371 Å °-0.0418 Å °-0.2126 Å °-0.05 Å °0.0113 Å °0.1645 Å °0.0861 Å °-0.0307 Å °
Refinement TLS groupSelection details: { A|* }

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