[English] 日本語
Yorodumi
- PDB-1j3f: Crystal Structure of an Artificial Metalloprotein:Cr(III)(3,3'-Me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j3f
TitleCrystal Structure of an Artificial Metalloprotein:Cr(III)(3,3'-Me2-salophen)/apo-A71G Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / myoglobin / asymmetric catalysis / crystal / Schiff bases / chromium / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CHROMIUM ION / Chem-CZM / PHOSPHATE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsKoshiyama, T. / Kono, M. / Ohashi, M. / Ueno, T. / Suzuki, A. / Yamane, T. / Watanabe, Y.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Coordinated Design of Cofactor and Active Site Structures in Development of New Protein Catalysts
Authors: Ueno, T. / Koshiyama, T. / Ohashi, M. / Kondo, K. / Kono, M. / Suzuki, A. / Yamane, T. / Watanabe, Y.
#1: Journal: Inorg.Chem. / Year: 2004
Title: Crystal Structures of Artificial Metalloproteins: Tight Binding of Fe(III)(Schiff-Base) by Mutation of Ala71 to Gly in Apo-Myoglobin.
Authors: Ueno, T. / Ohashi, M. / Kono, M. / Kondo, K. / Suzuki, A. / Yamane, T. / Watanabe, Y.
History
DepositionJan 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3189
Polymers17,3521
Non-polymers9668
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.972, 58.787, 76.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Myoglobin


Mass: 17352.123 Da / Num. of mol.: 1 / Mutation: A71G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: TB-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-CR / CHROMIUM ION


Mass: 51.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cr
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CZM / 'N,N'-BIS-(2-HYDROXY-3-METHYL-BENZYLIDENE)-BENZENE-1,2-DIAMINE' / 3,3'-ME2-SALOPHEN


Mass: 344.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.72 Å3/Da / Density % sol: 28.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium, potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 31, 2002
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. all: 26654 / Num. obs: 26426 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 40.6
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.9 / % possible all: 90

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1BVC

1bvc


Resolution: 1.45→30.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1798486.43 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1251 4.8 %RANDOM
Rwork0.194 ---
all0.196 26266 --
obs0.194 25855 95.6 %-
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 57 269 1531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION5CZM.PARAMCZM.TOP

+
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