[English] 日本語
Yorodumi
- PDB-5ice: Crystal structure of (S)-norcoclaurine 6-O-methyltransferase with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ice
TitleCrystal structure of (S)-norcoclaurine 6-O-methyltransferase with S-adenosyl-L-homocysteine and norlaudanosoline
Components(S)-norcoclaurine 6-O-methyltransferase
KeywordsTRANSFERASE / methyltransferase / benzylisoquinoline alkaloid
Function / homology
Function and homology information


(RS)-norcoclaurine 6-O-methyltransferase / (RS)-norcoclaurine 6-O-methyltransferase activity / alkaloid metabolic process / O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2H4 / : / S-ADENOSYL-L-HOMOCYSTEINE / (RS)-norcoclaurine 6-O-methyltransferase
Similarity search - Component
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsRobin, A.Y. / Graindorge, M. / Giustini, C. / Dumas, R. / Matringe, M.
Funding support France, 1items
OrganizationGrant numberCountry
INRA (French National Institute for Agricultural Research)P-BV-2 France
CitationJournal: Plant J. / Year: 2016
Title: Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids.
Authors: Robin, A.Y. / Giustini, C. / Graindorge, M. / Matringe, M. / Dumas, R.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (S)-norcoclaurine 6-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,63111
Polymers39,5321
Non-polymers1,09910
Water4,648258
1
A: (S)-norcoclaurine 6-O-methyltransferase
hetero molecules

A: (S)-norcoclaurine 6-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,26222
Polymers79,0632
Non-polymers2,19920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11370 Å2
ΔGint-48 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.720, 109.130, 40.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-403-

K

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein (S)-norcoclaurine 6-O-methyltransferase


Mass: 39531.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant)
Production host: Escherichia coli (E. coli)
References: UniProt: Q5C9L7, (RS)-norcoclaurine 6-O-methyltransferase

-
Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-2H4 / (1S)-1-(3,4-dihydroxybenzyl)-1,2,3,4-tetrahydroisoquinoline-6,7-diol


Mass: 287.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17NO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Peg3350, Sodium Chloride, Phosphate Citrate buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 43013 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 20.495 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.9
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.70.2494.5183.5
1.7-1.90.179.73197.6
1.9-2.20.08821.02199.9
2.2-2.60.04933.981100
2.6-3.60.03150.051100
3.6-5.60.02367.571100
5.6-8.60.02165.181100
8.60.01864.99197.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→43.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.607 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 2110 5 %RANDOM
Rwork0.1622 ---
obs0.1639 42189 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 45.09 Å2 / Biso mean: 14.28 Å2 / Biso min: 3.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å2-0 Å2
2---0.76 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.6→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 70 258 3060
Biso mean--14.39 21.51 -
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222972
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9834052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88424.867113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36715527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.635158
X-RAY DIFFRACTIONr_chiral_restr0.1330.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212192
X-RAY DIFFRACTIONr_mcbond_it1.5111.51823
X-RAY DIFFRACTIONr_mcangle_it2.43322966
X-RAY DIFFRACTIONr_scbond_it3.45831149
X-RAY DIFFRACTIONr_scangle_it5.0244.51067
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 115 -
Rwork0.233 2183 -
all-2298 -
obs--100 %

+
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