[English] 日本語
Yorodumi
- PDB-5dcw: Iridoid synthase from Catharanthus roseus - ligand free structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dcw
TitleIridoid synthase from Catharanthus roseus - ligand free structure
ComponentsIridoid synthase
KeywordsOXIDOREDUCTASE / Iridoid synthase / short chain dehydrogenase / NADPH-dependent / Catharanthus roseus
Function / homology
Function and homology information


(S)-8-oxocitronellyl enol synthase / monoterpenoid biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
: / PRISE-like Rossmann-fold domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCaputi, L. / Kries, H. / Stevenson, C.E.M. / Kamileen, M.O. / Sherden, N.H. / Geu-Flores, F. / Lawson, D.M. / O'Connor, S.E.
Funding support United Kingdom, Switzerland, 3items
OrganizationGrant numberCountry
European Research Council311363 United Kingdom
Swiss National Science Foundation155581 Switzerland
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural determinants of reductive terpene cyclization in iridoid biosynthesis.
Authors: Kries, H. / Caputi, L. / Stevenson, C.E. / Kamileen, M.O. / Sherden, N.H. / Geu-Flores, F. / Lawson, D.M. / O'Connor, S.E.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0205
Polymers41,7721
Non-polymers2484
Water5,639313
1
A: Iridoid synthase
hetero molecules

A: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,04010
Polymers83,5442
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_675x-y+4/3,-y+8/3,-z+2/31
Buried area3560 Å2
ΔGint21 kcal/mol
Surface area29900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.200, 141.200, 106.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1215-

HOH

-
Components

#1: Protein Iridoid synthase


Mass: 41771.969 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-388
Source method: isolated from a genetically manipulated source
Details: The crystallised protein contained residues 23-388 of the wild-type amino acid sequence. The sequence differed from database entry K7WDL7 by an Asp to Asn change at position 87. The N- ...Details: The crystallised protein contained residues 23-388 of the wild-type amino acid sequence. The sequence differed from database entry K7WDL7 by an Asp to Asn change at position 87. The N-terminus retained two residues from the nickel affinity cleavage site. The C-terminus had an additional three vector-derived residues.
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: K7WDL7, EC: 1.3.1.99
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→70.6 Å / Num. obs: 32009 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.041 / Net I/σ(I): 16.2 / Num. measured all: 325714 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.9510.20.9862.42367823300.7990.32499.7
8.5-70.68.80.02274.635564020.9990.00899.8

-
Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DCU

5dcu


Resolution: 1.9→70.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1783 / WRfactor Rwork: 0.1518 / FOM work R set: 0.8446 / SU B: 6.991 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1447 / SU Rfree: 0.1307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 1605 5 %RANDOM
Rwork0.1761 ---
obs0.1777 30404 99.95 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 89.5 Å2 / Biso mean: 30 Å2 / Biso min: 5.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.9→70.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 16 322 3134
Biso mean--36.46 32.73 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192945
X-RAY DIFFRACTIONr_bond_other_d0.0020.022740
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9424010
X-RAY DIFFRACTIONr_angle_other_deg0.96936320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03625.122123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07415478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.346156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02667
X-RAY DIFFRACTIONr_mcbond_it0.5871.1761470
X-RAY DIFFRACTIONr_mcbond_other0.5871.1751469
X-RAY DIFFRACTIONr_mcangle_it1.0251.7581845
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 101 -
Rwork0.264 2227 -
all-2328 -
obs--99.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.43370.5674-0.06036.4506-0.58545.1682-0.09460.1964-0.1867-0.407-0.0270.2580.44090.02950.12160.2030.04510.03680.0505-0.02220.0558-49.1055134.776426.7751
23.3592-3.1460.79045.9961-1.99012.2758-0.2618-0.0726-0.64530.20740.15280.89590.5406-0.42630.1090.2554-0.12580.17970.0987-0.07220.2449-62.2318143.019537.5938
31.0726-0.07150.79661.0703-0.80763.0367-0.02970.1405-0.0145-0.27390.11670.09630.4047-0.3131-0.08710.1317-0.0876-0.01860.09370.00850.0102-66.0661153.751620.4869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 140
2X-RAY DIFFRACTION2A141 - 214
3X-RAY DIFFRACTION3A215 - 391

+
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