[English] 日本語
Yorodumi
- PDB-7cb9: CYP76AH1/miltiradiene from Salvia miltiorrhiza -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cb9
TitleCYP76AH1/miltiradiene from Salvia miltiorrhiza
ComponentsFerruginol synthase
KeywordsPLANT PROTEIN / CYP76AH1 / tanshinone biosynthesis / miltiradiene / substrate specificity / molecular mechanism
Function / homology
Function and homology information


ferruginol synthase / diterpenoid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, E-class, group I / 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 / Miltiradiene / Ferruginol synthase
Similarity search - Component
Biological speciesSalvia miltiorrhiza (redroot sage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsChang, Z. / Chao, S. / Mingyue, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773833 China
CitationJournal: To Be Published
Title: CYP76AH1 from Salvia miltiorrhiza
Authors: Chang, Z.
History
DepositionJun 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferruginol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4823
Polymers55,5931
Non-polymers8892
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-17 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.500, 108.500, 105.685
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Ferruginol synthase / Cytochrome P450 76AH1


Mass: 55593.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia miltiorrhiza (redroot sage) / Gene: CYP76AH1 / Production host: Escherichia coli (E. coli) / References: UniProt: S4UX02, EC: 1.14.13.190
#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-J6C / Miltiradiene / (4bS,8aS)-4b,8,8-trimethyl-2-propan-2-yl-1,4,5,6,7,8a,9,10-octahydrophenanthrene


Mass: 272.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 50mM HEPES, pH7.5, 10% v/v Jeffamine M-600 Reagent, 50mM MnCl2, 25 % (v/v) glycerol

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 109634 / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.022 / Rrim(I) all: 0.098 / Χ2: 0.869 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9320.30.56928050.9560.1290.5840.506100
1.93-1.9720.50.47727960.9680.1080.4890.548100
1.97-2.0120.30.41628290.9740.0940.4270.565100
2.01-2.05200.36128540.9770.0820.370.619100
2.05-2.0919.70.30827790.9830.0710.3160.655100
2.09-2.1419.10.26628130.9860.0620.2740.706100
2.14-2.1918.10.23428440.9870.0560.2410.766100
2.19-2.2520.30.20928100.9920.0480.2150.819100
2.25-2.3220.70.18528340.9920.0420.190.897100
2.32-2.3920.60.16528280.9940.0370.1690.924100
2.39-2.4820.40.14728460.9950.0330.1510.969100
2.48-2.5820.30.13528270.9950.0310.1391.034100
2.58-2.719.90.11928430.9960.0270.1221.069100
2.7-2.8418.10.10828370.9960.0260.1111.056100
2.84-3.0220.70.09828680.9970.0220.11.042100
3.02-3.2520.90.08728390.9980.020.091.044100
3.25-3.5820.50.07628670.9980.0170.0781.004100
3.58-4.0918.60.06929140.9980.0160.0711.034100
4.09-5.1620.20.0629060.9980.0140.0621.053100
5.16-5018.70.05830350.9980.0140.061.0599.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YM3

5ym3


Resolution: 1.9→37.85 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2287 --
Rwork0.22 --
obs-66826 99.96 %
Displacement parametersBiso max: 82.51 Å2 / Biso min: 6.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3667 0 63 516 4246

+
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