[English] 日本語
Yorodumi
- PDB-5coa: Crystal structure of iridoid synthase at 2.2-angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5coa
TitleCrystal structure of iridoid synthase at 2.2-angstrom resolution
ComponentsIridoid synthase
KeywordsOXIDOREDUCTASE / SDR / P5bR / Rossmann fold / 1-4 addition
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
(S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQin, L. / Zhu, Y. / Ding, Z. / Zhang, X. / Ye, S. / Zhang, R.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structure of iridoid synthase in complex with NADP(+)/8-oxogeranial reveals the structural basis of its substrate specificity.
Authors: Qin, L. / Zhu, Y. / Ding, Z. / Zhang, X. / Ye, S. / Zhang, R.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iridoid synthase
B: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0957
Polymers82,4292
Non-polymers6675
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-74 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.290, 160.290, 85.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Iridoid synthase


Mass: 41214.305 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli (E. coli) / References: UniProt: K7WDL7, EC: 1.3.1.99
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.98 M ammonium sulfate, 1% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.2→38.9 Å / Num. obs: 56895 / % possible obs: 99.4 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6G

2v6g


Resolution: 2.2→38.9 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2879 5.07 %
Rwork0.1746 --
obs0.1763 56809 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5658 0 39 434 6131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055846
X-RAY DIFFRACTIONf_angle_d0.9237933
X-RAY DIFFRACTIONf_dihedral_angle_d12.1782126
X-RAY DIFFRACTIONf_chiral_restr0.062869
X-RAY DIFFRACTIONf_plane_restr0.004999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1968-2.23280.25491190.21762520X-RAY DIFFRACTION99
2.2328-2.27130.28571400.2032526X-RAY DIFFRACTION99
2.2713-2.31260.23491330.19572531X-RAY DIFFRACTION100
2.3126-2.35710.23871420.19152546X-RAY DIFFRACTION100
2.3571-2.40520.23771360.18692530X-RAY DIFFRACTION100
2.4052-2.45750.24121370.18462538X-RAY DIFFRACTION99
2.4575-2.51470.21151310.18112563X-RAY DIFFRACTION100
2.5147-2.57750.23481360.17762546X-RAY DIFFRACTION100
2.5775-2.64720.21751340.18272537X-RAY DIFFRACTION100
2.6472-2.72510.23461510.18142553X-RAY DIFFRACTION100
2.7251-2.8130.21831280.18072504X-RAY DIFFRACTION97
2.813-2.91350.2361290.18642567X-RAY DIFFRACTION100
2.9135-3.03010.22061340.1812584X-RAY DIFFRACTION100
3.0301-3.1680.22651160.17812603X-RAY DIFFRACTION100
3.168-3.33490.18621400.17242570X-RAY DIFFRACTION100
3.3349-3.54370.17961470.16242597X-RAY DIFFRACTION100
3.5437-3.81710.17861630.15492565X-RAY DIFFRACTION100
3.8171-4.20080.17191360.15652520X-RAY DIFFRACTION96
4.2008-4.80780.19731260.14932655X-RAY DIFFRACTION100
4.8078-6.05360.21011420.18192664X-RAY DIFFRACTION100
6.0536-100.20291590.18942711X-RAY DIFFRACTION97
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)
14.40030.3892-0.07472.20910.54934.25630.02380.3531-0.0006-0.22170.0851-0.255-0.31060.3519-0.1210.2528-0.06270.01630.18530.01120.20233.031459.009137.7467
22.36510.6042-0.28122.29880.67382.4014-0.0153-0.1193-0.25670.1328-0.0553-0.11440.0110.1010.09070.20430.04050.03430.18710.01130.181224.652946.737347.8128
31.1076-0.4479-0.61821.88051.19372.28980.01810.1682-0.123-0.1207-0.1378-0.0315-0.0182-0.15540.12860.14640.02340.03370.17920.00760.174219.474239.12327.9749
42.835-0.7502-0.55181.656-0.14210.831-0.03320.5509-0.5289-0.0565-0.09560.46480.109-0.39240.10110.208-0.0242-0.00670.5527-0.15050.3291-20.391345.322837.8045
51.2846-0.1677-0.3991.44-1.01452.331-0.14770.0586-0.30650.1214-0.01240.06790.157-0.27230.14850.2058-0.0450.08320.2397-0.06570.2582-5.498934.998452.0721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 387 )
4X-RAY DIFFRACTION4chain 'B' and (resid 27 through 214 )
5X-RAY DIFFRACTION5chain 'B' and (resid 215 through 387 )

+
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://pdbjlc1.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