[English] 日本語
Yorodumi
- PDB-8ho2: crystal structure of Norcoclaurine synthase from Chinese lotus (N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ho2
Titlecrystal structure of Norcoclaurine synthase from Chinese lotus (Nelumbo nucicera)
ComponentsS-norcoclaurine synthase
KeywordsPLANT PROTEIN / Benzylisoquinoline alkaloids biosynthesis / dimeric formation / enantioselectivity
Function / homology
Function and homology information


(S)-norcoclaurine synthase / (S)-norcoclaurine synthase activity / alkaloid metabolic process / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START-like domain superfamily
Similarity search - Domain/homology
S-norcoclaurine synthase
Similarity search - Component
Biological speciesNelumbo nucifera (sacred lotus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.711 Å
AuthorsLiao, L.J. / Zhao, Y.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81703637 China
National Natural Science Foundation of China (NSFC)31970596 China
CitationJournal: Acs Catalysis / Year: 2023
Title: Discovery, Structure, and Mechanism of the (R, S)-Norcoclaurine Synthase for the Chiral Synthesis of Benzylisoquinoline Alkaloids
Authors: Zhang, L. / Zhang, S. / Liao, L. / Tang, H. / Wang, W. / Yin, F. / Han, L. / Zhu, K. / Liu, Y. / Xu, D. / Wang, X. / Qin, M. / Xiao, Y. / Sheng, X. / Zhao, Y.
History
DepositionDec 9, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-norcoclaurine synthase
B: S-norcoclaurine synthase


Theoretical massNumber of molelcules
Total (without water)36,9052
Polymers36,9052
Non-polymers00
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-4 kcal/mol
Surface area14620 Å2
Unit cell
Length a, b, c (Å)47.262, 58.104, 114.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein S-norcoclaurine synthase / S-norcoclaurine synthase 1-like


Mass: 18452.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nelumbo nucifera (sacred lotus) / Gene: LOC104590414, HUJ06_019302 / Production host: Eschenbachia (plant) / References: UniProt: A0A191T7N6, (S)-norcoclaurine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 12.8 mM (NH4)2SO4, 8% PEG-3350, 10 mM betaine hydrochloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.711→19.379 Å / Num. obs: 64909 / % possible obs: 99.07 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.035 / Rrim(I) all: 0.126 / Net I/σ(I): 14.1
Reflection shellResolution: 1.711→1.7324 Å / Num. unique obs: 34476 / Rpim(I) all: 0.104

-
Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XDSdata scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NON

5non


Resolution: 1.711→19.379 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 3772 5.81 %
Rwork0.1566 --
obs0.1579 64909 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.711→19.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 0 356 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_chiral_restr0.067387
X-RAY DIFFRACTIONf_plane_restr0.005441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7792-1.80460.22231410.15752295X-RAY DIFFRACTION100
1.8046-1.83150.19971400.16912272X-RAY DIFFRACTION100
1.8315-1.86010.20461410.16262252X-RAY DIFFRACTION100
1.8601-1.89060.18661440.162335X-RAY DIFFRACTION100
1.8906-1.92310.20931440.15422283X-RAY DIFFRACTION100
1.9231-1.95810.19131350.15782272X-RAY DIFFRACTION100
1.9581-1.99570.19661440.162284X-RAY DIFFRACTION100
1.9957-2.03640.15581480.15442306X-RAY DIFFRACTION100
2.0364-2.08060.21471400.15542276X-RAY DIFFRACTION100
2.0806-2.1290.19281420.15682281X-RAY DIFFRACTION100
2.129-2.18210.20281390.15542258X-RAY DIFFRACTION100
2.1821-2.24110.18331370.1582333X-RAY DIFFRACTION100
2.2411-2.30690.19761420.15742264X-RAY DIFFRACTION100
2.3069-2.38120.18641380.15842289X-RAY DIFFRACTION100
2.3812-2.46620.18951440.15872275X-RAY DIFFRACTION100
2.4662-2.56470.16721370.1622288X-RAY DIFFRACTION100
2.5647-2.68120.21361410.16472288X-RAY DIFFRACTION100
2.6812-2.82210.19471380.16342280X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.6346 Å / Origin y: -27.0161 Å / Origin z: 14.3683 Å
111213212223313233
T0.0907 Å2-0.0006 Å20.0192 Å2-0.0911 Å20.0023 Å2--0.0727 Å2
L0.1886 °20.0478 °20.0737 °2-0.4783 °2-0.0664 °2---0.0248 °2
S0.0008 Å °-0.0003 Å °0.0047 Å °0.0155 Å °0.0166 Å °0.0263 Å °-0.0174 Å °-0.0083 Å °0.0001 Å °
Refinement TLS groupSelection details: all

+
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