[English] 日本語
Yorodumi
- PDB-1rse: MYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rse
TitleMYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D)
ComponentsHORSE HEART MYOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBurk, D.L. / Brayer, G.D.
Citation
Journal: Biochemistry / Year: 1996
Title: Electrostatic modification of the active site of myoglobin: characterization of the proximal Ser92Asp variant.
Authors: Lloyd, E. / Burk, D.L. / Ferrer, J.C. / Maurus, R. / Doran, J. / Carey, P.R. / Brayer, G.D. / Mauk, A.G.
#1: Journal: Protein Eng. / Year: 1991
Title: Expression in Escherichia Coli of a Synthetic Gene Coding for Horse Heart Myoglobin
Authors: Guillemette, J.G. / Matsushima-Hibiya, Y. / Atkinson, T. / Smith, M.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: High-Resolution Study of the Three-Dimensional Structure of Horse Heart Metmyoglobin
Authors: Evans, S.V. / Brayer, G.D.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Horse Heart Metmyoglobin. A 2.8-A Resolution Three-Dimensional Structure Determination
Authors: Evans, S.V. / Brayer, G.D.
#4: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
Authors: Sherwood, C. / Mauk, A.G. / Brayer, G.D.
History
DepositionJun 20, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HORSE HEART MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7243
Polymers17,0121
Non-polymers7132
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.420, 28.880, 35.970
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HORSE HEART MYOGLOBIN


Mass: 17011.525 Da / Num. of mol.: 1 / Mutation: S92D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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.: 61 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHOH 156 IS COVALENTLY BOUND TO THE IRON OF THE HEME.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
259 %satammonium sulfate1drop
320 mMTris-HCl1drop
41 mMEDTA1drop
567 %satammonium sulfate1reservoir
620 mMTris-HCl1reservoir
71 mMEDTA1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 28, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11967 / % possible obs: 85.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.059
Reflection
*PLUS
Num. measured all: 45864

-
Processing

Software
NameClassification
PROLSQrefinement
OSCILLdata reduction
RefinementResolution: 1.7→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.188 -
all-11615
obs-11615
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 0 66 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3761.5
X-RAY DIFFRACTIONp_mcangle_it2.1072.5
X-RAY DIFFRACTIONp_scbond_it2.3612
X-RAY DIFFRACTIONp_scangle_it3.7693
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.0480.06
X-RAY DIFFRACTIONp_singtor_nbd0.1930.2
X-RAY DIFFRACTIONp_multtor_nbd0.1590.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1470.2
X-RAY DIFFRACTIONp_planar_tor1.31.5
X-RAY DIFFRACTIONp_staggered_tor17.820
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3715
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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