[English] 日本語
Yorodumi
- PDB-8esu: Myoglobin variant Mb-imi complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8esu
TitleMyoglobin variant Mb-imi complex
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / HEME / METALLOPROTEIN / MYOGLOBIN / IMIDAZOLE
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsBacik, J.P. / Fasan, R. / Ando, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone.
Authors: Nam, D. / Bacik, J.P. / Khade, R.L. / Aguilera, M.C. / Wei, Y. / Villada, J.D. / Neidig, M.L. / Zhang, Y. / Ando, N. / Fasan, R.
History
DepositionOct 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1345
Polymers17,2561
Non-polymers8784
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.425, 90.425, 45.442
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

-
Components

#1: Protein Myoglobin


Mass: 17256.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: Mb(H64G,V68A) at 3.6 mM in 20 mM Tris-HCl pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution (200 mM Tris-HCl pH 8.9 and 2.46 M ammonium sulfate). The crystal was dunked ...Details: Mb(H64G,V68A) at 3.6 mM in 20 mM Tris-HCl pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution (200 mM Tris-HCl pH 8.9 and 2.46 M ammonium sulfate). The crystal was dunked in a cryoprotection solution (reservoir buffer supplemented with 9% sucrose (w/v), 2% glucose (w/v), 8% glycerol (v/v), and 8% ethylene glycol (v/v)) prior to being flash-frozen in liquid nitrogen. Note that imidazole was present in lysis buffer at 10 mM prior to two-step purification.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.04→78.31 Å / Num. obs: 101447 / % possible obs: 99.6 % / Redundancy: 9.2 % / Biso Wilson estimate: 8.65 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Net I/σ(I): 18.2
Reflection shellResolution: 1.04→1.06 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4642 / CC1/2: 0.817 / Rpim(I) all: 0.234

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M8F

6m8f


Resolution: 1.04→78.31 Å / SU ML: 0.0944 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 9.5982
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1406 5080 5.01 %
Rwork0.1284 96364 -
obs0.129 101444 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.27 Å2
Refinement stepCycle: LAST / Resolution: 1.04→78.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 58 281 1546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761360
X-RAY DIFFRACTIONf_angle_d1.01921850
X-RAY DIFFRACTIONf_chiral_restr0.0781193
X-RAY DIFFRACTIONf_plane_restr0.0064229
X-RAY DIFFRACTIONf_dihedral_angle_d14.4027504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.050.26831480.2622902X-RAY DIFFRACTION90.18
1.05-1.060.24281660.22763214X-RAY DIFFRACTION99.97
1.06-1.080.21541730.1893222X-RAY DIFFRACTION99.97
1.08-1.090.1621670.16363166X-RAY DIFFRACTION100
1.09-1.10.13741790.13773228X-RAY DIFFRACTION99.97
1.1-1.120.12821600.11663181X-RAY DIFFRACTION100
1.12-1.140.11021640.10963236X-RAY DIFFRACTION99.97
1.14-1.150.11781860.10383186X-RAY DIFFRACTION99.88
1.15-1.170.11111890.09933189X-RAY DIFFRACTION100
1.17-1.190.11661710.10293220X-RAY DIFFRACTION100
1.19-1.210.12631550.11023209X-RAY DIFFRACTION100
1.21-1.230.13581770.11813217X-RAY DIFFRACTION99.97
1.23-1.260.13611930.123194X-RAY DIFFRACTION99.94
1.26-1.280.1291710.1323214X-RAY DIFFRACTION99.97
1.28-1.310.14091570.12773212X-RAY DIFFRACTION99.91
1.31-1.340.13771510.10683234X-RAY DIFFRACTION100
1.34-1.370.11151740.10343220X-RAY DIFFRACTION100
1.37-1.410.11461460.10023235X-RAY DIFFRACTION99.94
1.41-1.450.10661330.10123251X-RAY DIFFRACTION100
1.45-1.50.11091760.09563206X-RAY DIFFRACTION100
1.5-1.550.12161560.10233256X-RAY DIFFRACTION99.97
1.55-1.610.11011720.1063218X-RAY DIFFRACTION99.82
1.61-1.690.12381660.1143238X-RAY DIFFRACTION100
1.69-1.780.13751690.12733239X-RAY DIFFRACTION100
1.78-1.890.13451700.12863225X-RAY DIFFRACTION100
1.89-2.030.12491640.13123223X-RAY DIFFRACTION99.82
2.03-2.240.13881660.12973243X-RAY DIFFRACTION99.56
2.24-2.560.14911910.1363234X-RAY DIFFRACTION100
2.56-3.230.15722160.14133231X-RAY DIFFRACTION100
3.23-78.310.15971740.1433321X-RAY DIFFRACTION99.23

+
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