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- PDB-5noi: human Robo2 extracellular domains 4-5 -

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Basic information

Entry
Database: PDB / ID: 5noi
Titlehuman Robo2 extracellular domains 4-5
ComponentsRoundabout homolog 2
KeywordsSIGNALING PROTEIN / Slit-Robo
Function / homology
Function and homology information


olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / ROBO receptors bind AKAP5 / axon guidance receptor activity / Regulation of commissural axon pathfinding by SLIT and ROBO / endocardial cushion formation ...olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / ROBO receptors bind AKAP5 / axon guidance receptor activity / Regulation of commissural axon pathfinding by SLIT and ROBO / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / metanephros development / aortic valve morphogenesis / retinal ganglion cell axon guidance / axon midline choice point recognition / aorta development / ureteric bud development / positive regulation of axonogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / axolemma / cellular response to hormone stimulus / central nervous system development / axon guidance / brain development / cell-cell adhesion / Regulation of expression of SLITs and ROBOs / chemotaxis / cell surface / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
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 ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Roundabout homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOpatowsky, Y. / Barak, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
ISF1425/15 Israel
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Robo Ig4 Is a Dimerization Domain.
Authors: Yom-Tov, G. / Barak, R. / Matalon, O. / Barda-Saad, M. / Guez-Haddad, J. / Opatowsky, Y.
History
DepositionApr 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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
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 2


Theoretical massNumber of molelcules
Total (without water)21,6881
Polymers21,6881
Non-polymers00
Water25214
1
A: Roundabout homolog 2

A: Roundabout homolog 2


Theoretical massNumber of molelcules
Total (without water)43,3752
Polymers43,3752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+3/2,y,-z+7/41
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.749, 99.749, 123.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Roundabout homolog 2


Mass: 21687.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO2, KIAA1568 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HCK4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.19 Å3/Da / Density % sol: 65.26 % / Description: pyramid
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 1.1M NaCl, 11-13% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.008818 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008818 Å / Relative weight: 1
ReflectionResolution: 2.4→38.8 Å / Num. obs: 12530 / % possible obs: 100 % / Redundancy: 12.5 % / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C4K, 2EDJ

4c4k

2edj


Resolution: 2.4→38.8 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.17
RfactorNum. reflection% reflection
Rfree0.2669 2328 9.99 %
Rwork0.2371 --
obs0.2401 23308 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 0 14 1490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231520
X-RAY DIFFRACTIONf_angle_d1.9152081
X-RAY DIFFRACTIONf_dihedral_angle_d16.664933
X-RAY DIFFRACTIONf_chiral_restr0.12246
X-RAY DIFFRACTIONf_plane_restr0.017273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3985-2.44750.40251360.38661224X-RAY DIFFRACTION100
2.4475-2.50070.3531380.37611223X-RAY DIFFRACTION100
2.5007-2.55890.43031400.35791239X-RAY DIFFRACTION100
2.5589-2.62290.38961400.341224X-RAY DIFFRACTION100
2.6229-2.69380.38921370.3731250X-RAY DIFFRACTION100
2.6938-2.7730.43551360.35411226X-RAY DIFFRACTION100
2.773-2.86250.43281370.36151238X-RAY DIFFRACTION100
2.8625-2.96480.33461360.33941234X-RAY DIFFRACTION100
2.9648-3.08350.33611350.32411224X-RAY DIFFRACTION100
3.0835-3.22380.32751360.26231243X-RAY DIFFRACTION100
3.2238-3.39370.35911330.27331243X-RAY DIFFRACTION100
3.3937-3.60630.35161390.25951238X-RAY DIFFRACTION100
3.6063-3.88460.25951390.23571221X-RAY DIFFRACTION100
3.8846-4.27530.20481400.18721241X-RAY DIFFRACTION100
4.2753-4.89330.1881340.16931233X-RAY DIFFRACTION100
4.8933-6.16280.19841390.1821234X-RAY DIFFRACTION100
6.1628-46.46190.20681330.19931245X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 99.9705 Å / Origin y: 102.0444 Å / Origin z: 131.1448 Å
111213212223313233
T0.503 Å2-0.042 Å2-0.0129 Å2-0.3618 Å20.0299 Å2--0.2885 Å2
L0.2169 °20.1463 °20.2748 °2-1.3024 °2-0.073 °2--0.3624 °2
S-0.0354 Å °-0.098 Å °0.2026 Å °0.4393 Å °-0.0121 Å °0.0338 Å °-0.1565 Å °-0.1576 Å °0.0192 Å °
Refinement TLS groupSelection details: all

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