[English] 日本語
Yorodumi
- PDB-2mb5: HYDRATION IN PROTEIN CRYSTALS. A NEUTRON DIFFRACTION ANALYSIS OF ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mb5
TitleHYDRATION IN PROTEIN CRYSTALS. A NEUTRON DIFFRACTION ANALYSIS OF CARBONMONOXYMYOGLOBIN
ComponentsMYOGLOBIN
KeywordsOXYGEN 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
CARBON MONOXIDE / DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / AMMONIUM CATION WITH D / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodNEUTRON DIFFRACTION / Resolution: 1.8 Å
AuthorsSchoenborn, B.P. / Cheng, X.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Hydration in Protein Crystals. A Neutron Diffraction Analysis of Carbonmonoxymyoglobin
Authors: Cheng, X. / Schoenborn, B.P.
#1: Journal: J.Mol.Biol. / Year: 1981
Title: Real Space Refinement of Neutron Diffraction Data from Sperm Whale Carbonmonoxymyoglobin
Authors: Hanson, J.C. / Schoenborn, B.P.
#2: Journal: Acs Symp.Ser. / Year: 1980
Title: The Determination of Structural Water by Neutron Protein Crystallography. An Analysis of the Carbon Monoxide Myoglobin Water Structure
Authors: Schoenborn, B.P. / Hanson, J.C.
#3: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1975
Title: Neutron Diffraction Analysis and Real Space Refinement of met and Carbon Monoxide Myoglobin
Authors: Schoenborn, B.P. / Norvell, J.C.
#4: Journal: Brookhaven Symposia in Biology / Year: 1975
Title: Neutron Diffraction Analysis of Metmyoglobin
Authors: Schoenborn, B.P. / Diamond, R.
#5: Journal: Science / Year: 1975
Title: Neutron Diffraction Analysis of Myoglobin. Structure of the Carbon Monoxide Derivative
Authors: Norvell, J.C. / Nunes, A.C. / Schoenborn, B.P.
#6: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: A Neutron Diffraction Analysis of Myoglobin. III. Hydrogen-Deuterium Bonding in Side Chains
Authors: Schoenborn, B.P.
#7: Journal: Nature / Year: 1969
Title: Neutron Diffraction Analysis of Myoglobin
Authors: Schoenborn, B.P.
#8: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionOct 11, 1989Processing site: BNL
SupersessionJan 15, 1991ID: 1MB5
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0869
Polymers17,2351
Non-polymers8518
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.610, 30.950, 34.860
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein MYOGLOBIN /


Mass: 17234.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185

-
Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ND4 / AMMONIUM CATION WITH D


Mass: 22.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#6: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: D2O

-
Experimental details

-
Experiment

ExperimentMethod: NEUTRON DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
Method: unknown

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 55 89 1361
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONp_bond_d0.006
NEUTRON DIFFRACTIONp_angle_d0.039

+
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