[English] 日本語
Yorodumi
- PDB-4m4i: Radiation damage study of Cu T6-insulin - 0.12 MGy -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m4i
TitleRadiation damage study of Cu T6-insulin - 0.12 MGy
Components(Insulin) x 2
KeywordsHORMONE / Copper binding
Function / homology
Function and homology information


positive regulation of blood circulation / estradiol secretion / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of lactation / positive regulation of cell maturation / response to L-arginine / response to butyrate / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite ...positive regulation of blood circulation / estradiol secretion / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of lactation / positive regulation of cell maturation / response to L-arginine / response to butyrate / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to food / feeding behavior / positive regulation of Rho protein signal transduction / response to growth hormone / positive regulation of peptide hormone secretion / protein secretion / positive regulation of insulin secretion / negative regulation of lipid catabolic process / response to glucose / response to nutrient levels / positive regulation of protein secretion / hormone activity / insulin receptor binding / glucose metabolic process / positive regulation of phosphatidylinositol 3-kinase signaling / response to heat / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / Insulin, conserved site / Insulin family signature.
Similarity search - Domain/homology
COPPER (II) ION / Insulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFrankaer, C.G. / Harris, P. / Stahl, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T6 bovine insulin derivatives.
Authors: Frankaer, C.G. / Mossin, S. / Stahl, K. / Harris, P.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,6146
Polymers11,4874
Non-polymers1272
Water1,02757
1
A: Insulin
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8073
Polymers5,7442
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-16 kcal/mol
Surface area3590 Å2
MethodPISA
2
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8073
Polymers5,7442
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-15 kcal/mol
Surface area3590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.643, 80.643, 33.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

CU

21D-101-

CU

31B-218-

HOH

41B-220-

HOH

51D-214-

HOH

-
Components

#1: Protein/peptide Insulin /


Mass: 2339.645 Da / Num. of mol.: 2 / Fragment: INSULIN A CHAIN (UNP RESIDUES 85-105) / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#2: Protein/peptide Insulin /


Mass: 3403.927 Da / Num. of mol.: 2 / Fragment: INSULIN B CHAIN (UNP RESIDUES 25-54) / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / 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: 1.82 Å3/Da / Density % sol: 32.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.05M sodium citrate, 15%(v/v) acetone, 7.5mM copper(II)acetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 14, 2013
RadiationMonochromator: Multilayered mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→16.75 Å / Num. all: 6368 / Num. obs: 6340 / % possible obs: 99.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.1

-
Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→16.746 Å / SU ML: 0.17 / σ(F): 2.02 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 312 4.92 %Random
Rwork0.1654 ---
obs0.1673 6337 99.64 %-
all-6368 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→16.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 2 57 853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008838
X-RAY DIFFRACTIONf_angle_d1.0471131
X-RAY DIFFRACTIONf_dihedral_angle_d17.171293
X-RAY DIFFRACTIONf_chiral_restr0.077125
X-RAY DIFFRACTIONf_plane_restr0.004147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.39310.25761590.19623012X-RAY DIFFRACTION100
2.3931-16.74650.17831530.15253013X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.4144-2.1602-4.03096.4862-0.48128.08040.17150.5704-0.90610.1609-0.2471-0.3420.9889-0.45390.02670.4350.0166-0.07440.2209-0.05280.2629-8.7414-11.596-13.3067
26.95052.38681.71455.272-4.52596.83230.0787-0.2179-0.5636-0.042-0.1258-0.16570.6524-0.31930.04280.1724-0.0745-0.07230.1739-0.00860.2812-16.0741-12.0344-4.3649
33.73121.4623-4.44893.7388-3.86927.1313-0.1135-0.45810.0962-0.002-0.17480.0101-0.04760.62640.23670.10330.0029-0.04330.12820.00330.0834-6.4181-6.9076-1.3381
46.0408-2.4635-2.77364.83780.98714.109-0.11740.2546-0.1245-0.31550.21880.32410.7042-0.3812-0.0950.2007-0.0465-0.03610.0880.02720.1237-4.2637-16.96860.254
57.23824.07325.22325.53483.3794.1385-0.0707-1.081-0.47680.9828-0.3033-0.23750.44130.20460.42760.34030.05530.01930.34190.07190.13522.4628-14.345913.0973
69.58756.62023.55979.72510.39146.8877-0.01150.2547-0.39770.5780.4033-0.3902-0.05190.5584-0.34220.3750.12410.03770.2234-0.01830.20938.4469-18.2124.2988
74.2684-2.2172-2.96657.81556.14625.24380.20820.04060.1-0.2679-0.0678-0.0584-0.1549-0.0236-0.1460.140.0274-0.02440.10080.01490.11362.2755-9.45230.7957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:8 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 13:19 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 9:18 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 23:27 ) OR CHAIN D AND (RESID 23:27 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 1:8 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 13:19 )
7X-RAY DIFFRACTION7CHAIN D AND (RESID 9:18 )

+
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