[English] 日本語
Yorodumi
- PDB-8tdp: Time-resolved SFX-XFEL crystal structure of CYP121 bound with cYY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tdp
TitleTime-resolved SFX-XFEL crystal structure of CYP121 bound with cYY reacted with peracetic acid for 200 milliseconds
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / SFX / room temperature / ES complex / P450
Function / homology
Function and homology information


mycocyclosin synthase / cyclase activity / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / carbon monoxide binding / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROGEN PEROXIDE / Chem-YTT / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNguyen, R.C. / Dasgupta, M. / Bhowmick, A. / Kern, J.F. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108988 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121.
Authors: Nguyen, R.C. / Davis, I. / Dasgupta, M. / Wang, Y. / Simon, P.S. / Butryn, A. / Makita, H. / Bogacz, I. / Dornevil, K. / Aller, P. / Bhowmick, A. / Chatterjee, R. / Kim, I.S. / Zhou, T. / ...Authors: Nguyen, R.C. / Davis, I. / Dasgupta, M. / Wang, Y. / Simon, P.S. / Butryn, A. / Makita, H. / Bogacz, I. / Dornevil, K. / Aller, P. / Bhowmick, A. / Chatterjee, R. / Kim, I.S. / Zhou, T. / Mendez, D. / Paley, D.W. / Fuller, F. / Alonso Mori, R. / Batyuk, A. / Sauter, N.K. / Brewster, A.S. / Orville, A.M. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Liu, A.
History
DepositionJul 4, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionNov 22, 2023ID: 7RUK
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6329
Polymers43,1751
Non-polymers1,4578
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.728, 78.728, 265.884
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-764-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43174.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp121, Rv2276, MTCY339.34c / Plasmid: pET28a-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPP7, mycocyclosin synthase

-
Non-polymers , 5 types, 293 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-YTT / (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione / cyclo(tyrosyl-tyrosyl) / Cyclo(tyr-tyr)


Mass: 326.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2 M ammonium sulfate, 100 mM MES buffer pH 5.3

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.300614 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Mar 24, 2021 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.300614 Å / Relative weight: 1
ReflectionResolution: 1.85→33.18 Å / Num. obs: 42794 / % possible obs: 99.86 % / Redundancy: 8.16 % / Biso Wilson estimate: 29.07 Å2 / CC1/2: 0.841 / Net I/σ(I): 3.01
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.16 % / Mean I/σ(I) obs: 0.587 / Num. unique obs: 2095 / CC1/2: 0.257 / % possible all: 98.85

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
cctbx.xfeldata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.18 Å / SU ML: 0.2473 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2278 1991 4.67 %
Rwork0.1811 40619 -
obs0.1833 42610 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.21 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 94 285 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793229
X-RAY DIFFRACTIONf_angle_d1.04324415
X-RAY DIFFRACTIONf_chiral_restr0.0568497
X-RAY DIFFRACTIONf_plane_restr0.0082572
X-RAY DIFFRACTIONf_dihedral_angle_d7.5491444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.36871310.32852738X-RAY DIFFRACTION96.05
1.9-1.950.33891390.31552813X-RAY DIFFRACTION98.89
1.95-20.3261380.28362841X-RAY DIFFRACTION99.73
2-2.070.28681410.26512868X-RAY DIFFRACTION99.9
2.07-2.140.2561390.24382822X-RAY DIFFRACTION99.93
2.14-2.230.27941410.22872865X-RAY DIFFRACTION100
2.23-2.330.26041410.222882X-RAY DIFFRACTION100
2.33-2.450.22721420.2132891X-RAY DIFFRACTION99.93
2.45-2.610.28011410.19792873X-RAY DIFFRACTION100
2.61-2.810.23971430.19062915X-RAY DIFFRACTION100
2.81-3.090.25571440.18392925X-RAY DIFFRACTION100
3.09-3.540.2121450.15182950X-RAY DIFFRACTION100
3.54-4.460.17511470.12933010X-RAY DIFFRACTION100
4.46-33.180.17991590.14343226X-RAY DIFFRACTION99.97

+
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