[English] 日本語
Yorodumi
- PDB-6kfw: The cytochrome P450 enzyme CxnD for C-S bond formation in chuangx... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kfw
TitleThe cytochrome P450 enzyme CxnD for C-S bond formation in chuangxinmycin biosynthesis
ComponentsCxnD
KeywordsOXIDOREDUCTASE / P450 / CxnD
Function / homologyChem-D8L / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesActinoplanes tsinanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHong, B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: The Cytochrome P450 Catalyzing C-S Bond Formation in S-Heterocyclization of Chuangxinmycin Biosynthesis.
Authors: Shi, Y. / Jiang, Z. / Hu, X. / Hu, X. / Gu, R. / Jiang, B. / Zuo, L. / Li, X. / Sun, H. / Zhang, C. / Wang, L. / Wu, L. / Hong, B.
History
DepositionJul 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 9, 2022Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Nov 22, 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: CxnD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5136
Polymers45,3731
Non-polymers1,1405
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-39 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.460, 76.291, 80.029
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 CxnD


Mass: 45372.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes tsinanensis (bacteria) / 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-D8L / (2R)-3-(1H-indol-3-yl)-2-methylsulfanyl-propanoic acid


Mass: 235.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29784 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.051 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1312 / Rpim(I) all: 0.198 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHW

2whw


Resolution: 2→25.88 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.4137 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2383 1474 4.97 %
Rwork0.1823 28156 -
obs0.1851 29630 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.96 Å2
Refinement stepCycle: LAST / Resolution: 2→25.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 74 278 3521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01713322
X-RAY DIFFRACTIONf_angle_d2.58784540
X-RAY DIFFRACTIONf_chiral_restr0.2368508
X-RAY DIFFRACTIONf_plane_restr0.0103590
X-RAY DIFFRACTIONf_dihedral_angle_d19.11581248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.24481290.21042424X-RAY DIFFRACTION95.8
2.06-2.140.23441290.18942543X-RAY DIFFRACTION100
2.14-2.220.24361160.172563X-RAY DIFFRACTION100
2.22-2.320.22291150.16652552X-RAY DIFFRACTION100
2.32-2.450.24221350.17772548X-RAY DIFFRACTION100
2.45-2.60.23841400.17852548X-RAY DIFFRACTION100
2.6-2.80.26231450.18592560X-RAY DIFFRACTION100
2.8-3.080.27291390.19832574X-RAY DIFFRACTION99.96
3.08-3.530.22521630.18622554X-RAY DIFFRACTION99.89
3.53-4.440.21341540.16392605X-RAY DIFFRACTION99.6
4.44-25.880.2511090.19152685X-RAY DIFFRACTION97.28

+
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://pdbjlvh1.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