[English] 日本語
Yorodumi
- PDB-4xav: Crystal structure of olfactomedin domain from gliomedin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xav
TitleCrystal structure of olfactomedin domain from gliomedin
ComponentsGliomedin
KeywordsCELL ADHESION / beta propeller / 5 bladed propeller / olfactomedin
Function / homology
Function and homology information


clustering of voltage-gated sodium channels / protein binding involved in heterotypic cell-cell adhesion / microvillus organization / collagen trimer / membrane => GO:0016020 / axon / cell surface / extracellular space / plasma membrane
Similarity search - Function
Gliomedin / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
PHOSPHATE ION / Gliomedin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.052 Å
AuthorsHill, S.E. / Nguyen, E. / Lieberman, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: Plos One / Year: 2015
Title: Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies.
Authors: Hill, S.E. / Donegan, R.K. / Nguyen, E. / Desai, T.M. / Lieberman, R.L.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gliomedin
B: Gliomedin
C: Gliomedin
D: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,76319
Polymers123,6354
Non-polymers1,12815
Water14,448802
1
A: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2145
Polymers30,9091
Non-polymers3054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1164
Polymers30,9091
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1224
Polymers30,9091
Non-polymers2133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3126
Polymers30,9091
Non-polymers4035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.164, 140.643, 78.152
Angle α, β, γ (deg.)90.00, 106.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Gliomedin / Cancer-related gene liver 2 protein / CRG-L2


Mass: 30908.846 Da / Num. of mol.: 4 / Fragment: UNP residues 279-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gldn, Crgl2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BMF8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: phosphate citrate pH 5.5 PEG 600

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→44.65 Å / Num. obs: 59953 / % possible obs: 98.2 % / Redundancy: 5.2 % / Net I/σ(I): 9.05

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000phasing
PHENIXmodel building
PHENIXphasing
RefinementResolution: 2.052→44.646 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1998 3.34 %
Rwork0.1662 --
obs0.1678 59848 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.052→44.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7900 0 62 802 8764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058155
X-RAY DIFFRACTIONf_angle_d0.92411039
X-RAY DIFFRACTIONf_dihedral_angle_d13.0742890
X-RAY DIFFRACTIONf_chiral_restr0.0371188
X-RAY DIFFRACTIONf_plane_restr0.0041388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.052-2.10310.23431380.17173920X-RAY DIFFRACTION94
2.1031-2.15990.26851440.18194082X-RAY DIFFRACTION97
2.1599-2.22350.23151390.18274120X-RAY DIFFRACTION98
2.2235-2.29520.25311380.18034106X-RAY DIFFRACTION98
2.2952-2.37730.23121480.17834184X-RAY DIFFRACTION98
2.3773-2.47240.24221410.18514135X-RAY DIFFRACTION98
2.4724-2.58490.27781450.18354090X-RAY DIFFRACTION98
2.5849-2.72120.2741390.18594136X-RAY DIFFRACTION98
2.7212-2.89170.23351430.18534150X-RAY DIFFRACTION99
2.8917-3.11490.24551480.18374154X-RAY DIFFRACTION99
3.1149-3.42830.18911440.15584188X-RAY DIFFRACTION99
3.4283-3.92410.1841430.1464203X-RAY DIFFRACTION99
3.9241-4.94290.14461470.13144186X-RAY DIFFRACTION99
4.9429-44.65610.20291410.17514196X-RAY DIFFRACTION98

+
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://pdbjlc1.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