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- PDB-2v70: Third LRR domain of human Slit2 -

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Basic information

Entry
Database: PDB / ID: 2v70
TitleThird LRR domain of human Slit2
ComponentsSLIT HOMOLOG 2 PROTEIN N-PRODUCT
KeywordsSTRUCTURAL PROTEIN / NEUROGENESIS / GLYCOPROTEIN / SLIT2 / SECRETED / CHEMOTAXIS / LRR DOMAIN / DIFFERENTIATION / EGF-LIKE DOMAIN / LEUCINE-RICH REPEAT / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


negative regulation of leukocyte chemotaxis / corticospinal neuron axon guidance through spinal cord / negative regulation of lamellipodium assembly / induction of negative chemotaxis / negative regulation of mononuclear cell migration / negative regulation of retinal ganglion cell axon guidance / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis / chemorepulsion involved in postnatal olfactory bulb interneuron migration / Roundabout binding ...negative regulation of leukocyte chemotaxis / corticospinal neuron axon guidance through spinal cord / negative regulation of lamellipodium assembly / induction of negative chemotaxis / negative regulation of mononuclear cell migration / negative regulation of retinal ganglion cell axon guidance / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis / chemorepulsion involved in postnatal olfactory bulb interneuron migration / Roundabout binding / negative regulation of smooth muscle cell chemotaxis / negative regulation of cellular response to growth factor stimulus / cellular response to heparin / negative regulation of small GTPase mediated signal transduction / negative regulation of chemokine-mediated signaling pathway / response to cortisol / laminin-1 binding / negative regulation of smooth muscle cell migration / axon extension involved in axon guidance / Formation of the ureteric bud / Netrin-1 signaling / GTPase inhibitor activity / Role of ABL in ROBO-SLIT signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of neutrophil chemotaxis / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / Inactivation of CDC42 and RAC1 / negative regulation of actin filament polymerization / Signaling by ROBO receptors / pulmonary valve morphogenesis / negative regulation of vascular permeability / aortic valve morphogenesis / cell migration involved in sprouting angiogenesis / Activation of RAC1 / motor neuron axon guidance / proteoglycan binding / negative regulation of endothelial cell migration / ureteric bud development / negative chemotaxis / positive regulation of axonogenesis / retinal ganglion cell axon guidance / branching morphogenesis of an epithelial tube / ventricular septum morphogenesis / cellular response to hormone stimulus / negative regulation of cell migration / negative regulation of protein phosphorylation / axon guidance / negative regulation of cell growth / Regulation of expression of SLITs and ROBOs / heparin binding / positive regulation of apoptotic process / calcium ion binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / cytoplasm
Similarity search - Function
Leucine rich repeat C-terminal domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Leucine rich repeat N-terminal domain / Cystine knot, C-terminal ...Leucine rich repeat C-terminal domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Leucine rich repeat N-terminal domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Laminin G domain profile. / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Laminin G domain / Laminin G domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Epidermal growth factor-like domain. / Leucine-rich repeat profile. / EGF-like domain profile. / EGF-like domain signature 2. / Leucine-rich repeat / EGF-like domain signature 1. / EGF-like domain / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Alpha Beta
Similarity search - Domain/homology
Slit homolog 2 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsMorlot, C. / Cusack, S. / McCarthy, A.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Production of Slit2 Lrr Domains in Mammalian Cells for Structural Studies and the Structure of Human Slit2 Domain 3.
Authors: Morlot, C. / Hemrika, W. / Romijn, R.A. / Gros, P. / Cusack, S. / Mccarthy, A.A.
History
DepositionJul 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
B: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
C: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
D: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4318
Polymers99,5464
Non-polymers8854
Water00
1
A: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1082
Polymers24,8861
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1082
Polymers24,8861
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1082
Polymers24,8861
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1082
Polymers24,8861
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.650, 96.860, 87.150
Angle α, β, γ (deg.)90.00, 95.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A505 - 1001
2111B505 - 1001
3111C505 - 1001
4111D505 - 1001

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.39951, 0.1912, 0.89657), (0.21232, -0.93212, 0.29339), (0.8918, 0.30757, 0.33179)18.31262, -16.73755, -29.73543
3given(-0.99923, -0.03916, 0.003), (-0.03431, 0.83332, -0.55172), (0.01911, -0.5514, -0.83402)43.82039, -11.2099, -39.62059
4given(0.31831, -0.30817, -0.8965), (-0.1977, -0.94647, 0.25516), (-0.92714, 0.09601, -0.3622)44.20992, -32.39871, 20.42708

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Components

#1: Protein
SLIT HOMOLOG 2 PROTEIN N-PRODUCT / SLIT-2


Mass: 24886.449 Da / Num. of mol.: 4 / Fragment: THIRD LRR DOMAIN, RESIDUES 504-714
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATION ON N623 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O94813
#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.: 4
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

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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: 2.7 Å3/Da / Density % sol: 54.6 % / Description: NONE
Crystal growpH: 5.6
Details: 15% PEG 4000, 0.2M NH4 ACETATE, 0.1M NACITRATE, PH=5.6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 22, 2005 / Details: TORODIAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 45165 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODIFIED PDB ENTRY 1W8A

1w8a


Resolution: 3.01→30 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.869 / SU B: 50.217 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1008 5.1 %RANDOM
Rwork0.222 ---
obs0.225 18760 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.97 Å2
Baniso -1Baniso -2Baniso -3
1--4.35 Å20 Å2-3.2 Å2
2--7.78 Å20 Å2
3----4.02 Å2
Refinement stepCycle: LAST / Resolution: 3.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6495 0 56 0 6551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226687
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9739088
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2855836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.15825.354297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.074151138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4581531
X-RAY DIFFRACTIONr_chiral_restr0.1090.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024979
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.22639
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.24467
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.421.54266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71726759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32332653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2294.52329
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1604 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.090.05
3Ctight positional0.070.05
4Dtight positional0.070.05
1Atight thermal0.10.5
2Btight thermal0.110.5
3Ctight thermal0.110.5
4Dtight thermal0.110.5
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.494 75
Rwork0.444 1315
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)
13.0398-0.09172.1591.4071-0.036710.55880.0072-0.0325-0.1060.3299-0.06570.02460.3804-0.0930.0585-0.26840.03320.044-0.1757-0.0344-0.11487.5349-13.95643.9374
27.08692.02034.82282.86262.60826.9290.16170.40720.2690.05640.0006-0.29940.04650.1621-0.1623-0.12480.05580.1189-0.3728-0.0232-0.088434.95965.75332.3268
34.78370.86431.25774.56652.48317.05470.01220.1853-0.2636-0.45760.0251-0.02540.44250.3457-0.0372-0.18380.01370.0655-0.38420.0364-0.130737.153-24.9143-34.8316
47.91640.32755.72480.84650.39097.87430.1549-0.28410.0056-0.1064-0.02020.04960.0122-0.8316-0.1347-0.14520.0580.0705-0.2190.0325-0.20550.0185-7.720843.4935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A505 - 714
2X-RAY DIFFRACTION2B505 - 714
3X-RAY DIFFRACTION3C505 - 714
4X-RAY DIFFRACTION4D505 - 714

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