[English] 日本語
Yorodumi
- PDB-7slh: Engineered sperm whale myoglobin-based carbene transferase MbBTIC-C3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7slh
TitleEngineered sperm whale myoglobin-based carbene transferase MbBTIC-C3
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / METALLOPROTEIN / MYOGLOBIN / HEME / TRANSFERASE / OXYGEN TRANSPORT
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 / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsJenkins, J.L. / Vargas, D. / Ren, X. / Fasan, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM98628 United States
CitationJournal: Nat.Chem. / Year: 2024
Title: Biocatalytic strategy for the construction of sp 3 -rich polycyclic compounds from directed evolution and computational modelling.
Authors: Vargas, D.A. / Ren, X. / Sengupta, A. / Zhu, L. / Roy, S. / Garcia-Borras, M. / Houk, K.N. / Fasan, R.
History
DepositionOct 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6229
Polymers17,3331
Non-polymers1,2898
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.519, 90.519, 45.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-206-

SO4

21A-551-

HOH

31A-616-

HOH

41A-620-

HOH

51A-673-

HOH

-
Components

#1: Protein Myoglobin


Mass: 17333.094 Da / Num. of mol.: 1 / Mutation: L29F, H64V, V68A, I107L, N122D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 2.4 M Ammonium Sulfate, 20 mM Tris-HCl pH 8.8, 0.1 mM EDTA

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.05 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2021
Details: RH COATED COLLIMATING MIRRORS, K-B FOCUSING MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.15→39.27 Å / Num. obs: 135716 / % possible obs: 96.4 % / Redundancy: 8.8 % / CC1/2: 0.998 / Rpim(I) all: 0.025 / Net I/σ(I): 15.9
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2538 / CC1/2: 0.918 / Rpim(I) all: 0.153 / % possible all: 68.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSFeb 5, 2021data reduction
Aimless0.7.4data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.15→39.27 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 10.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1257 6830 5.03 %
Rwork0.1071 128886 -
obs0.108 135716 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.7 Å2 / Biso mean: 14.2805 Å2 / Biso min: 5.06 Å2
Refinement stepCycle: final / Resolution: 1.15→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 118 407 1732
Biso mean--16.92 28.18 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.160.17091390.18992562270155
1.16-1.180.16891550.15033005316064
1.18-1.190.16981670.13853310347770
1.19-1.210.15081800.13193523370376
1.21-1.220.14892020.12113742394480
1.22-1.240.14081940.11993897409184
1.24-1.260.13161950.10924129432487
1.26-1.280.12372600.11014375463594
1.28-1.30.12152250.10254547477296
1.3-1.320.13412790.10484401468096
1.32-1.340.12342560.10254459471596
1.34-1.360.11162230.10734548477196
1.36-1.390.11631990.09974517471696
1.39-1.420.11022240.09784471469596
1.42-1.450.09712430.09154540478397
1.45-1.480.0992290.09044542477197
1.48-1.520.11812210.09034530475197
1.52-1.560.11222830.08934571485497
1.56-1.610.11762070.08924569477698
1.61-1.660.11572710.09284512478397
1.66-1.720.10822420.09454588483098
1.72-1.790.11842480.09924510475898
1.79-1.870.12352700.09914577484798
1.87-1.970.1132330.10134678491198
1.97-2.090.10832470.09614555480299
2.09-2.250.10932330.09984659489299
2.25-2.480.12972290.09774643487299
2.48-2.840.13162710.1134626489799
2.84-3.570.13522500.11394628487899
3.57-39.270.15132550.13294672492799

+
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