[English] 日本語
Yorodumi
- PDB-2zou: Crystal structure of human F-spondin reeler domain (fragment 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zou
TitleCrystal structure of human F-spondin reeler domain (fragment 2)
ComponentsSpondin-1
KeywordsCELL ADHESION / beta-sandwich / extracellular protein / 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 / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Reeler domain / Spondin_N / Spondin domain profile. / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Spondin-like TSP1 domain ...Reeler domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Reeler domain / 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 / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,0668
Polymers33,6942
Non-polymers3726
Water3,963220
1
A: Spondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0955
Polymers16,8471
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Spondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9713
Polymers16,8471
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.253, 50.518, 63.171
Angle α, β, γ (deg.)90.00, 100.37, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 16846.859 Da / Num. of mol.: 2 / Fragment: reeler domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPON1, KIAA0762, VSGP / Cell line (production host): HEK293S cell / Production host: Homo sapiens (human) / References: UniProt: Q9HCB6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.85 %
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

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 48350 / % possible obs: 94.5 % / Redundancy: 3.7 % / Rsym value: 0.069 / Net I/σ(I): 15.1
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.433 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZOT

2zot


Resolution: 1.45→62.14 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.38 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22248 2430 5 %RANDOM
Rwork0.20203 ---
obs0.20306 45897 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0.23 Å2
2--1.01 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.45→62.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 24 220 2439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222342
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9623157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.73322.564117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87215410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8851526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021756
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21037
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21623
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.51423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28322265
X-RAY DIFFRACTIONr_scbond_it1.90231032
X-RAY DIFFRACTIONr_scangle_it2.8884.5892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.452→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 188 -
Rwork0.23 3285 -
obs--92.99 %
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)
10.7892-0.22380.00860.65420.1382.1083-0.0159-0.00190.00290.0387-0.0444-0.0644-0.03470.2910.0603-0.05380.00070.0026-0.00310.0244-0.028710.2713-0.33622.9662
21.04540.02370.2851.0084-0.00821.59-0.01660.06220.0099-0.095-0.05070.0575-0.0461-0.03840.0673-0.03720.01430.002-0.03920.0001-0.0329-16.4751-0.4348.2007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 184
2X-RAY DIFFRACTION2B43 - 184

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more