[English] 日本語
Yorodumi
- PDB-5emh: Crystal structure of Iridoid Synthase from Cantharanthus roseus i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5emh
TitleCrystal structure of Iridoid Synthase from Cantharanthus roseus in complex with NADP+
ComponentsIridoid synthase
KeywordsOXIDOREDUCTASE / Reductase / Complex / NADPH
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
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSandholu, A. / Thulasiram, H.V. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRBSC0124 India
CitationJournal: FEBS Lett. / Year: 2018
Title: Dynamics of loops at the substrate entry channel determine the specificity of iridoid synthases.
Authors: Sandholu, A.S. / Mohole, M. / Duax, W.L. / Thulasiram, H.V. / Sengupta, D. / Kulkarni, K.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Other
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4342
Polymers41,6911
Non-polymers7431
Water3,621201
1
A: Iridoid synthase
hetero molecules

A: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8684
Polymers83,3822
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)66.861, 66.861, 173.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

21A-667-

HOH

-
Components

#1: Protein Iridoid synthase


Mass: 41690.809 Da / Num. of mol.: 1 / Fragment: UNP residues 21-388 / Mutation: P175Q/V198I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Plasmid: pTHREE-E / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: K7WDL7, EC: 1.3.1.99
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 4000, Trisodium citrate, MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.1→47.28 Å / Num. obs: 23849 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.036 / Net I/σ(I): 21.1 / Num. measured all: 281155 / Scaling rejects: 2
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
2.1-2.16120.79242293019100.890.235100
8.91-47.289.30.02368.8368139710.00899.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.2.8data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6F

2v6f


Resolution: 2.1→43.678 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1219 5.13 %
Rwork0.1823 22553 -
obs0.184 23772 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.93 Å2 / Biso mean: 30.2085 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 2.1→43.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 48 201 3055
Biso mean--24.27 38.87 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022931
X-RAY DIFFRACTIONf_angle_d0.7833986
X-RAY DIFFRACTIONf_chiral_restr0.029437
X-RAY DIFFRACTIONf_plane_restr0.003497
X-RAY DIFFRACTIONf_dihedral_angle_d14.2071068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1001-2.18420.28521170.213524422559
2.1842-2.28360.30731400.223424372577
2.2836-2.4040.25891490.19724552604
2.404-2.55460.24031340.190824632597
2.5546-2.75180.22221500.188724522602
2.7518-3.02860.21211430.180624932636
3.0286-3.46670.18061260.156625222648
3.4667-4.36710.18611290.155925542683
4.3671-43.68710.20271310.196727352866
Refinement TLS params.Method: refined / Origin x: 73.0006 Å / Origin y: 77.3784 Å / Origin z: 26.9342 Å
111213212223313233
T0.2031 Å20.004 Å20.0186 Å2-0.2258 Å20.0186 Å2--0.2114 Å2
L1.2616 °20.1725 °2-0.1043 °2-0.8407 °2-0.2574 °2--1.1409 °2
S-0.089 Å °0.1229 Å °0.0222 Å °-0.0731 Å °0.0136 Å °-0.0624 Å °0.0928 Å °0.0336 Å °0.0634 Å °
Refinement TLS groupSelection details: (chain A and resseq 34:395)

+
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