[English] 日本語
Yorodumi
- PDB-1a6n: DEOXY-MYOGLOBIN, ATOMIC RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a6n
TitleDEOXY-MYOGLOBIN, ATOMIC RESOLUTION
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME PROTEIN / MODEL COMPOUNDS / OXYGEN STORAGE / LIGAND BINDING GEOMETRY / CONFORMATIONAL SUBSTATES
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsVojtechovsky, J. / Chu, K. / Berendzen, J. / Sweet, R.M. / Schlichting, I.
CitationJournal: Biophys.J. / Year: 1999
Title: Crystal structures of myoglobin-ligand complexes at near-atomic resolution.
Authors: Vojtechovsky, J. / Chu, K. / Berendzen, J. / Sweet, R.M. / Schlichting, I.
History
DepositionFeb 26, 1998Processing site: BNL
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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)17,8584
Polymers17,0501
Non-polymers8093
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.760, 30.660, 34.310
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MYOGLOBIN /


Mass: 17049.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
250 mg/mlmyoglobin11
350 mMpotassium phosphate11
1ammonium sulfate11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jan 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 45065 / % possible obs: 98 % / Observed criterion σ(I): -3 / Rsym value: 0.052 / Net I/σ(I): 24
Reflection shellResolution: 1.15→1.2 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.216 / % possible all: 98
Reflection
*PLUS
Num. measured all: 378009 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.216

-
Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MBC

1mbc


Resolution: 1.15→8 Å / Num. parameters: 14248 / Num. restraintsaints: 48770 / Cross valid method: FREE R-VALUE
StereochEM target val spec case: HEME - PARAMETERS BASED ON CSD
Stereochemistry target values: ENGH & HUBER
Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. AQUOMET CONTAMINATION CORRECTED BY 30% OCCUPIED MODEL OF AQUOMET MYOGLOBIN. BAYESIAN DIFFERENCE REFINEMENT WAS USED ...Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. AQUOMET CONTAMINATION CORRECTED BY 30% OCCUPIED MODEL OF AQUOMET MYOGLOBIN. BAYESIAN DIFFERENCE REFINEMENT WAS USED AT THE FINAL STEP. SEE TERWILLIGER AND BERENDZEN, ACTA CRYST. D52:1004-1011 (1996). THE SOLVENT MOLECULES 81, 129, 139 AND 151 CAN BE MODELED ONLY FOR ONE ALTERNATIVE PROTEIN CONFORMATION.
RfactorNum. reflection% reflection
Rfree0.1454 2219 5 %
all0.1225 44565 -
obs0.1213 -97 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 1263.5 / Occupancy sum non hydrogen: 1424.1
Refinement stepCycle: LAST / Resolution: 1.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 53 186 1575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.074

+
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