[English] 日本語
Yorodumi
- PDB-1f63: CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f63
TitleCRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / myoglobin / heme / triple mutant / 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 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 speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBrunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H.
Citation
Journal: Biophys.J. / Year: 1999
Title: Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10).
Authors: Brunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H.
#1: Journal: TRENDS BIOCHEM.SCI. / Year: 1999
Title: Does Picosecond Protein Dynamics Have a Survival Value?
Authors: Brunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Role of Cavities in Protein Dynamics: Crystal Structure of a Photolytic Intermediate of a Mutant Myoglobin
Authors: Brunori, M. / Vallone, B. / Cutruzzola, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / Sweet, R.M. / Schlichting, I.
History
DepositionJun 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 7, 2024Group: 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)18,1743
Polymers17,4611
Non-polymers7132
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.520, 91.520, 45.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein MYOGLOBIN


Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: L29Y, H64Q, T67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#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.: 90 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTriple Mb mutant designed to mimick the properties of Ascaris suum Hb. The amino acid in the heme ...Triple Mb mutant designed to mimick the properties of Ascaris suum Hb. The amino acid in the heme distal site do not allow ligand binding to the heme without movement of the mutated Y(B10) and Q(E7)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 2.7 M Ammonium sulphate, 20 mM Tris-Cl, 1 mM EDTA, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMprotein1drop
210 mMsodium dithionite1drop
32.7 Mammonium sulfate1reservoir
420 mMTris-Cl1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 60982 / Num. obs: 19613 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13
Reflection shellResolution: 1.8→15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.249 / Num. unique all: 1079 / % possible all: 89.3
Reflection shell
*PLUS
% possible obs: 89.3 %

-
Processing

Software
NameVersionClassification
FFT(POINT MUTANT)model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
FFT(POINT MUTANT)phasing
RefinementResolution: 1.8→15 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: PROTIN
RfactorNum. reflection% reflectionSelection details
Rfree0.22 980 -random
Rwork0.169 ---
all0.172 19600 --
obs0.17 19600 94.3 %-
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 48 90 1370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.0143
X-RAY DIFFRACTIONp_angle_d1.2
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.2

+
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