[English] 日本語
Yorodumi
- PDB-8kfj: Crystal structure of sperm whale myoglobin (F46L/H64A mutant) rec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8kfj
TitleCrystal structure of sperm whale myoglobin (F46L/H64A mutant) reconstituted with manganese porphycene
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / globin fold / oxygen transport / muscles
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 / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PORPHYCENE CONTAINING MN / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMizohata, E. / Oohora, K. / Hayashi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Rational Design of an Artificial Ethylbenzene Hydroxylase Using Molecular Dynamics Simulation to Enhance the Enantioselectivity
Authors: Oohora, K. / Kagawa, Y. / Nishiura, T. / Mizohata, E. / Schwaneberg, U. / Hayashi, T.
History
DepositionAug 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,09818
Polymers38,5752
Non-polymers2,52316
Water4,432246
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5199
Polymers19,2871
Non-polymers1,2318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5799
Polymers19,2871
Non-polymers1,2928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.673, 80.174, 106.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Myoglobin


Mass: 19287.311 Da / Num. of mol.: 2 / Mutation: F46L,H64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02185
#2: Chemical ChemComp-HNN / PORPHYCENE CONTAINING MN


Mass: 619.612 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36MnN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate, 100 mM Tris-HCl buffer at pH 8.2, 4% acetone and 10% trehalose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39037 / % possible obs: 99.9 % / Redundancy: 6.63 % / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2472 / CC1/2: 0.607

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.36 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21242 1849 4.7 %RANDOM
Rwork0.17862 ---
obs0.18024 37124 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---1.62 Å20 Å2
3---2.6 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 152 246 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172613
X-RAY DIFFRACTIONr_angle_refined_deg3.9451.6893764
X-RAY DIFFRACTIONr_angle_other_deg1.5631.6196069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86423.333123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61915503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.056159
X-RAY DIFFRACTIONr_chiral_restr0.10.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022979
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02530
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2564.4261284
X-RAY DIFFRACTIONr_mcbond_other4.2244.421282
X-RAY DIFFRACTIONr_mcangle_it5.4216.6051603
X-RAY DIFFRACTIONr_mcangle_other5.3956.6061603
X-RAY DIFFRACTIONr_scbond_it5.9685.2381487
X-RAY DIFFRACTIONr_scbond_other5.6865.1251433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5797.3822080
X-RAY DIFFRACTIONr_long_range_B_refined9.99384.59111831
X-RAY DIFFRACTIONr_long_range_B_other9.98384.31411647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 155 -
Rwork0.307 2691 -
obs--99.96 %

+
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