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- PDB-2zot: Crystal structure of human F-spondin reeler domain (fragment 1) -

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Basic information

Entry
Database: PDB / ID: 2zot
TitleCrystal structure of human F-spondin reeler domain (fragment 1)
ComponentsSpondin-1
KeywordsCELL ADHESION / beta-sandwich / extracellular protein / Extracellular matrix / Glycoprotein / Secreted
Function / homology
Function and homology information


Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / extracellular matrix structural constituent / LBD domain binding / extracellular matrix / cell adhesion / endoplasmic reticulum lumen / : / metal ion binding
Similarity search - Function
Reeler domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Spondin_N / Spondin domain profile. / : / Reeler domain / Reeler domain / Reeler domain superfamily / Reelin domain profile. ...Reeler domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Spondin_N / Spondin domain profile. / : / Reeler domain / 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: 2.7 Å
AuthorsNagae, M. / Nogi, T. / Takagi, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of the F-spondin reeler domain reveals a unique beta-sandwich fold with a deformable disulfide-bonded loop
Authors: Nagae, M. / Nishikawa, K. / Yasui, N. / Yamasaki, M. / Nogi, T. / Takagi, J.
History
DepositionJun 7, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Dec 21, 2016Group: Structure summary
Revision 1.4Nov 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,6514
Polymers77,6514
Non-polymers00
Water00
1
A: Spondin-1


Theoretical massNumber of molelcules
Total (without water)19,4131
Polymers19,4131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Spondin-1


Theoretical massNumber of molelcules
Total (without water)19,4131
Polymers19,4131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Spondin-1


Theoretical massNumber of molelcules
Total (without water)19,4131
Polymers19,4131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Spondin-1


Theoretical massNumber of molelcules
Total (without water)19,4131
Polymers19,4131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.579, 57.579, 190.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 19412.717 Da / Num. of mol.: 4 / Fragment: reeler domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPON1, KIAA0762, VSGP / Plasmid: pcDNA3.1/Myc-His(+) vector / Cell line (production host): HEK293T cell / Production host: Homo sapiens (human) / References: UniProt: Q9HCB6
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M bis-tris(pH 5.5), 0.4M ammonium acetate, 25% polyethylene glycol(PEG) 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory BL-17A21.07225
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 20, 2006
ADSC QUANTUM 2702CCDFeb 21, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.072251
ReflectionResolution: 2.7→100 Å / Num. all: 17075 / Num. obs: 16670 / % possible obs: 100 % / Redundancy: 4.9 % / Rsym value: 0.083 / Net I/av σ(I): 7.3 / Net I/σ(I): 9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.038 / Num. unique all: 1724 / Rsym value: 0.488 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→57.54 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.835 / SU B: 43.47 / SU ML: 0.398 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31251 848 5.1 %RANDOM
Rwork0.24203 ---
obs0.24563 15792 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.96 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.7→57.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 0 0 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224511
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9616099
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50722.19210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30515754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6371552
X-RAY DIFFRACTIONr_chiral_restr0.0780.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023440
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23068
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3141.52860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56124507
X-RAY DIFFRACTIONr_scbond_it0.7631842
X-RAY DIFFRACTIONr_scangle_it1.2824.51592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 62 -
Rwork0.303 1198 -
obs--99.68 %
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)
14.42622.5203-2.43868.1597-4.8944.8413-0.44770.5951-0.2704-0.62170.376-0.14220.5045-0.25750.0718-0.1965-0.0984-0.00930.01980.0091-0.1565-10.6532-6.99660.9912
26.993.3523-2.07044.8482-2.76584.30580.4836-0.9167-0.54880.39-0.6716-0.5721-0.16920.36570.1881-0.2811-0.1108-0.05810.12710.2765-0.079717.02449.7281-1.6898
37.79252.4765-4.8015.4133-2.49385.07890.4067-0.7314-0.10560.621-0.4916-0.2301-0.29960.55930.0849-0.0427-0.1051-0.0007-0.2176-0.0143-0.192135.896439.404427.2469
45.02752.3688-2.09238.5152-1.79183.4981-0.67260.3594-0.5251-0.85640.5575-0.64150.4246-0.1260.11510.1077-0.14060.2609-0.2619-0.0712-0.14819.067911.892329.8287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 184
2X-RAY DIFFRACTION2B38 - 183
3X-RAY DIFFRACTION3C44 - 184
4X-RAY DIFFRACTION4D38 - 183

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