[English] 日本語
Yorodumi
- PDB-7ddr: Ancestral myoglobin aMbSp of Puijila Darwini relative (imidazol l... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ddr
TitleAncestral myoglobin aMbSp of Puijila Darwini relative (imidazol ligand)
ComponentsAncestral myoglobin aMbSp
KeywordsOXYGEN STORAGE / Protein evolution / Ancestral protein / Diving adaptation / Seals
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsIsogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K. / Shirai, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H01818 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101111j0004 Japan
CitationJournal: Iscience / Year: 2021
Title: Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals.
Authors: Isogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K.I. / Shirai, T.
History
DepositionOct 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ancestral myoglobin aMbSp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8423
Polymers17,1571
Non-polymers6862
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-18 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.020, 62.720, 65.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Ancestral myoglobin aMbSp


Mass: 17156.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 26.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M MIB buffer pH 5, 25% w/v PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 19228 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 13.96 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 18.3
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.04 / Num. unique obs: 2752

-
Processing

Software
NameVersionClassification
PHENIX1.17rc5_3630refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.17rc5_3630phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YCE

5yce


Resolution: 1.5→20 Å / SU ML: 0.1783 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 963 5.04 %
Rwork0.1644 18130 -
obs0.1662 19093 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.46 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 48 136 1393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01371318
X-RAY DIFFRACTIONf_angle_d1.30181785
X-RAY DIFFRACTIONf_chiral_restr0.0687180
X-RAY DIFFRACTIONf_plane_restr0.0065228
X-RAY DIFFRACTIONf_dihedral_angle_d25.2138494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.31321750.26282492X-RAY DIFFRACTION99.37
1.58-1.680.2751370.22862544X-RAY DIFFRACTION99.3
1.68-1.810.30741150.20222563X-RAY DIFFRACTION99.41
1.81-1.990.21841440.16462549X-RAY DIFFRACTION99.37
1.99-2.280.17761200.14642598X-RAY DIFFRACTION99.63
2.28-2.870.15691260.14512640X-RAY DIFFRACTION99.71
2.87-19.920.18031460.15092744X-RAY DIFFRACTION100

+
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