[English] 日本語
Yorodumi
- PDB-3ogb: Sperm whale myoglobin mutant H64W deoxy-form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ogb
TitleSperm whale myoglobin mutant H64W deoxy-form
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin / ligand migration pathways / oxygen storage
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / 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 / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsBirukou, I. / Soman, J. / Olson, J.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Blocking the gate to ligand entry in human hemoglobin.
Authors: Birukou, I. / Soman, J. / Olson, J.S.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,89411
Polymers17,4131
Non-polymers1,48110
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.830, 47.130, 88.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Myoglobin /


Mass: 17413.225 Da / Num. of mol.: 1 / Mutation: H65W
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 RESISTANT TB1 / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 9
Details: Solution of MB (carbonmonoxy-form) (20mg/ml protein in 0.02M TRIS-HCl pH 9.0) mixed with mother liquor (3.2M ammonium sulphate, 0.05M TRIS-HCl, pH 9.0) for final concentrations of 2.5M ...Details: Solution of MB (carbonmonoxy-form) (20mg/ml protein in 0.02M TRIS-HCl pH 9.0) mixed with mother liquor (3.2M ammonium sulphate, 0.05M TRIS-HCl, pH 9.0) for final concentrations of 2.5M ammonium sulphate to obtain crystals of MBCO. MBCO crystals were oxidyzed by excess of potassium ferricyanide, washed in mother liquor and reduced under anaerobic conditions with sodium dithionite, SMALL TUBES, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 23, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→23.57 Å / Num. obs: 21466 / % possible obs: 96.6 % / Redundancy: 3.65 % / Rmerge(I) obs: 0.043 / Χ2: 0.95 / Net I/σ(I): 15.5 / Scaling rejects: 695
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured all% possible all
1.6-1.663.660.2634.1198891
1.66-1.723.630.2584.7189491.4
1.72-1.83.550.2165.5205293.4
1.8-1.93.530.1716.5207894.5
1.9-2.023.480.1278.7213597.5
2.02-2.173.480.09811.1219699
2.17-2.393.710.07914219599
2.39-2.733.790.05918.62234100
2.73-3.443.840.0427.2225699.2
3.44-23.573.750.02745.9234898.4

-
Processing

Software
NameVersionClassificationNB
d*TREK9.9.3Ldata processing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3NML
Resolution: 1.6→23.565 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 1055 4.92 %RANDOM
Rwork0.1798 ---
obs0.1809 21429 96.38 %-
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.122 Å2 / ksol: 0.435 e/Å3
Displacement parametersBiso max: 73.49 Å2 / Biso mean: 20.7404 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.9137 Å2-0 Å2-0 Å2
2---0.4889 Å2-0 Å2
3----0.4248 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 88 249 1566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061475
X-RAY DIFFRACTIONf_angle_d1.0882021
X-RAY DIFFRACTIONf_chiral_restr0.07198
X-RAY DIFFRACTIONf_plane_restr0.003252
X-RAY DIFFRACTIONf_dihedral_angle_d14.507542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.67280.54691080.46012375248391
1.6728-1.7610.37391210.32942377249892
1.761-1.87130.30561290.23812422255194
1.8713-2.01570.21681100.17312567267797
2.0157-2.21840.18251220.16992610273299
2.2184-2.5390.19711610.162926112772100
2.539-3.19770.19311610.161826482809100
3.1977-23.56750.15571430.15352764290799

+
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