[English] 日本語
Yorodumi
- PDB-2oh8: Myoglobin cavity mutant I28W -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oh8
TitleMyoglobin cavity mutant I28W
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / MYOGLOBIN / LIGAND ENTRY AND EXIT PATHWAYS / 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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPhillips Jr., G.N. / Soman, J. / Olson, J.S.
CitationJournal: Iubmb Life / Year: 2007
Title: Ligand pathways in myoglobin: A review of trp cavity mutations.
Authors: Olson, J.S. / Soman, J. / Phillips, G.N.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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.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_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2474
Polymers17,4381
Non-polymers8093
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.438, 91.438, 45.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Myoglobin


Mass: 17438.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): Phage-resistent TB1 / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PROTEIN SOLUTION (20 MG/ML PROTEIN, 0.020 M TRIS-HCL, pH9.0), MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (2.8 M AMMONIUM SULPHATE, 0.050 M TRIS-HCL, pH9.0). cryo-protected with 20% SUCROSE, ...Details: PROTEIN SOLUTION (20 MG/ML PROTEIN, 0.020 M TRIS-HCL, pH9.0), MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (2.8 M AMMONIUM SULPHATE, 0.050 M TRIS-HCL, pH9.0). cryo-protected with 20% SUCROSE, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 12, 2000
RadiationMonochromator: MULTI-LAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→45.89 Å / Num. obs: 20060 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Redundancy: 4.25 % / Biso Wilson estimate: 15.2 Å2 / Limit h max: 43 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 24 / Limit l min: 0 / Observed criterion F max: 353951.59 / Observed criterion F min: 0.31 / Rmerge(I) obs: 0.039 / Χ2: 1.56 / Net I/σ(I): 14.8 / Scaling rejects: 1538
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.8-1.861.410.1683.9296621021.8553.1
1.86-1.941.860.1464.7560030021.5875.4
1.94-2.032.60.1195.8923035411.5189.2
2.03-2.133.750.09871458438791.5597.5
2.13-2.274.890.0798.61958739901.5199.6
2.27-2.445.180.06310.82066439761.5399.5
2.44-2.695.210.05113.22076539641.4299.6
2.69-3.085.210.04116.72066739511.4299.7
3.08-3.885.250.02923.62100639681.6599.8
3.88-45.94.990.02230.22076639621.8799

-
Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.89 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18 944 4.8 %random
Rwork0.156 ---
all-20488 --
obs-19861 96.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 54.5001 Å2 / ksol: 0.362338 e/Å3
Displacement parametersBiso max: 66.41 Å2 / Biso mean: 19.34 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.74 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.08 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 53 142 1425
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_torsion_deg18.7
X-RAY DIFFRACTIONx_torsion_impr_deg1.12
X-RAY DIFFRACTIONx_mcbond_it1.451.5
X-RAY DIFFRACTIONx_mcangle_it2.042
X-RAY DIFFRACTIONx_scbond_it2.962
X-RAY DIFFRACTIONx_scangle_it4.582.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.207783.80.18719970.0232521207582.3
1.88-1.980.1851094.40.15923510.0182548246096.5
1.98-2.110.1971234.90.1624030.0182552252699
2.11-2.270.1671224.80.14524170.0152558253999.3
2.27-2.50.1631234.80.14624150.0152558253899.2
2.5-2.860.1781335.20.15824050.0152558253899.2
2.86-3.60.2021295.10.16424220.0182569255199.3
3.6-45.890.1681274.80.1525070.0152650263499.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2heme-ferric.paramheme-ferric.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.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