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- PDB-1w8a: Third LRR domain of Drosophila Slit -

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Basic information

Entry
Database: PDB / ID: 1w8a
TitleThird LRR domain of Drosophila Slit
ComponentsSLIT PROTEIN
KeywordsSIGNALING PROTEIN / SECRETED PROTEIN / AXON GUIDANCE / LEUCINE-RICH REPEAT GLYCOPROTEIN / EGF-LIKE DOMAIN / SIGNAL PROTEIN
Function / homology
Function and homology information


Slit-Robo signaling complex / Role of ABL in ROBO-SLIT signaling / mesodermal cell migration / induction of negative chemotaxis / Signaling by ROBO receptors / mesoderm migration involved in gastrulation / synaptic target inhibition / regulation of epithelial cell migration, open tracheal system / digestive tract mesoderm development / salivary gland boundary specification ...Slit-Robo signaling complex / Role of ABL in ROBO-SLIT signaling / mesodermal cell migration / induction of negative chemotaxis / Signaling by ROBO receptors / mesoderm migration involved in gastrulation / synaptic target inhibition / regulation of epithelial cell migration, open tracheal system / digestive tract mesoderm development / salivary gland boundary specification / Roundabout binding / epithelial cell migration, open tracheal system / gonad development / glial cell migration / positive regulation of cell-cell adhesion / regulation of epithelial cell migration / Roundabout signaling pathway / embryonic heart tube development / axon midline choice point recognition / dendrite morphogenesis / outflow tract morphogenesis / axon guidance / neuron migration / neuron differentiation / heparin binding / positive regulation of cell migration / axon / calcium ion binding / cell surface / extracellular region / plasma membrane
Similarity search - Function
Leucine rich repeat C-terminal domain / 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 C-terminal domain / 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 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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. / Growth factor receptor cysteine-rich domain superfamily / 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
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHowitt, J.A. / Clout, N.J. / Hohenester, E.
CitationJournal: Embo J. / Year: 2004
Title: Binding Site for Robo Receptors Revealed by Dissection of the Leucine-Rich Repeat Region of Slit.
Authors: Howitt, J.A. / Clout, N.J. / Hohenester, E.
History
DepositionSep 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2017Group: Advisory / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SLIT PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,3131
Polymers21,3131
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)121.213, 31.852, 49.526
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SLIT PROTEIN


Mass: 21313.307 Da / Num. of mol.: 1 / Fragment: THIRD LRR DOMAIN, RESIDUES 542-733
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PCEP-PU / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: P24014
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.2 Å3/Da / Density % sol: 44.19 %

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 4705 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 7 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OZN

1ozn


Resolution: 2.8→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 493 10.3 %RANDOM
Rwork0.1994 ---
obs0.1994 4705 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.6057 Å2 / ksol: 0.294686 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.417 Å20 Å2-1.61 Å2
2--0.528 Å20 Å2
3---7.889 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 0 5 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
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_it0.8171
X-RAY DIFFRACTIONc_mcangle_it1.4411.5
X-RAY DIFFRACTIONc_scbond_it2.2392
X-RAY DIFFRACTIONc_scangle_it3.483
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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