[English] 日本語
Yorodumi
- PDB-8i74: Crystal structure of decarboxylated osteocalcin at pH 8.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i74
TitleCrystal structure of decarboxylated osteocalcin at pH 8.5
ComponentsOsteocalcin
KeywordsSTRUCTURAL PROTEIN / Ca-binding protein
Function / homology
Function and homology information


structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / type B pancreatic cell proliferation / regulation of bone mineralization / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus ...structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / type B pancreatic cell proliferation / regulation of bone mineralization / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus / bone development / brain development / hormone activity / cognition / osteoblast differentiation / cellular response to insulin stimulus / glucose homeostasis / learning or memory / calcium ion binding / extracellular region / cytoplasm
Similarity search - Function
Osteocalcin/matrix Gla protein / Osteocalcin / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues.
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsYokoyama, T. / Nabeshima, Y. / Obita, T. / Mizuguchi, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor
Authors: Mizuguchi, M. / Yokoyama, T. / Otani, T. / Kuribara, S. / Nabeshima, Y. / Obita, T. / Hirata, M. / Kawano, K.
History
DepositionJan 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Osteocalcin
B: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)8,4952
Polymers8,4952
Non-polymers00
Water1,02757
1
A: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)4,2481
Polymers4,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)4,2481
Polymers4,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.799, 42.799, 37.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein/peptide Osteocalcin / Bone Gla protein / BGP / Gamma-carboxyglutamic acid-containing protein


Mass: 4247.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: BGLAP / Production host: Escherichia coli (E. coli) / References: UniProt: P02820
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.05 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→42.8 Å / Num. obs: 14857 / % possible obs: 99.85 % / Redundancy: 8.11 % / CC1/2: 0.999 / Rrim(I) all: 0.039 / Net I/σ(I): 29.5
Reflection shellResolution: 1.36→1.41 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1481 / CC1/2: 0.922 / Rrim(I) all: 0.51

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→30.263 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 743 5 %
Rwork0.1761 --
obs0.1768 14855 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→30.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms546 0 0 57 603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006580
X-RAY DIFFRACTIONf_angle_d0.871786
X-RAY DIFFRACTIONf_dihedral_angle_d26.696230
X-RAY DIFFRACTIONf_chiral_restr0.0775
X-RAY DIFFRACTIONf_plane_restr0.005110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.46420.17741470.16162802X-RAY DIFFRACTION100
1.4642-1.61150.2021480.15292803X-RAY DIFFRACTION100
1.6115-1.84470.18811480.14532825X-RAY DIFFRACTION100
1.8447-2.3240.22361480.18372813X-RAY DIFFRACTION100
2.324-30.2630.17591520.18512869X-RAY DIFFRACTION99

+
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