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- PDB-3coo: The crystal structure of Reelin-N domain of F-spondin -

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Basic information

Entry
Database: PDB / ID: 3coo
TitleThe crystal structure of Reelin-N domain of F-spondin
ComponentsSpondin-1
KeywordsCELL ADHESION / F-spondin / reelin-N domain / Extracellular matrix / Glycoprotein / Secreted
Function / homology
Function and homology information


positive regulation of amyloid precursor protein catabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / positive regulation of protein processing / extracellular matrix structural constituent / LBD domain binding / negative regulation of amyloid-beta formation / extracellular matrix / protein processing / cell adhesion ...positive regulation of amyloid precursor protein catabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / positive regulation of protein processing / extracellular matrix structural constituent / LBD domain binding / negative regulation of amyloid-beta formation / extracellular matrix / protein processing / cell adhesion / endoplasmic reticulum lumen / extracellular space / metal ion binding
Similarity search - Function
Reeler domain / Reeler domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Spondin_N / Spondin domain profile. / : / Reeler domain / Reeler domain superfamily / Reelin domain profile. ...Reeler domain / Reeler domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Spondin_N / Spondin domain profile. / : / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Spondin-like TSP1 domain / Spondin-like TSP1 domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTan, K. / Lawler, J. / Wang, J.H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The crystal structure of the heparin-binding reelin-N domain of f-spondin.
Authors: Tan, K. / Duquette, M. / Liu, J.H. / Lawler, J. / Wang, J.H.
History
DepositionMar 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spondin-1
B: Spondin-1


Theoretical massNumber of molelcules
Total (without water)40,9982
Polymers40,9982
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-2.5 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.605, 58.605, 219.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-212-

HOH

21B-221-

HOH

DetailsDomain is a monomer in solution. Chains A and B may form a low affinity and fast off rate dimer.

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Components

#1: Protein Spondin-1 / F-spondin / Vascular smooth muscle cell growth-promoting factor


Mass: 20498.869 Da / Num. of mol.: 2 / Fragment: Reelin-N domain (UNP residues 29-194)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Homo sapiens / Plasmid: pMT/BiP V5-HisA / Cell line (production host): S2 cell / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9HCB6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium sulfate, 30% (W/V) PEG 4000, 0.1M Sodium Citrate tribasic dehydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2005 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 26814 / Num. obs: 26814 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 36.58
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4 / Num. unique all: 2485 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→40.06 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.458 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24111 1346 5 %RANDOM
Rwork0.20586 ---
all0.20762 25408 --
obs0.20762 25408 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 0 153 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222350
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9673189
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4915293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64222.456114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69815408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2671527
X-RAY DIFFRACTIONr_chiral_restr0.1810.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021807
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2991
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21584
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1461.51472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82222323
X-RAY DIFFRACTIONr_scbond_it2.8543995
X-RAY DIFFRACTIONr_scangle_it4.2554.5859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 80 -
Rwork0.23 1721 -
obs-1801 92.69 %
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)
13.772-0.0057-0.31833.05292.38463.69210.0213-0.1769-0.04660.193-0.02080.12760.1845-0.1209-0.0006-0.3357-0.00390.00250.0274-0.181-0.19716.83447.51636.251
23.4267-0.3498-0.33153.12332.2883.6705-0.1604-0.4039-0.07110.2043-0.029-0.02890.4369-0.11330.1894-0.2706-0.02730.0651-0.0633-0.1289-0.202215.52924.12213.96
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA39 - 18517 - 163
2X-RAY DIFFRACTION2BB42 - 18520 - 163

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