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- PDB-8ho2: crystal structure of Norcoclaurine synthase from Chinese lotus (N... -

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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 / 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: To Be Published
Title: The crystal structure of Norcoclaurine synthase from Chinese lotus (Nelumbo nucicera) was investigated to determine its catalytic mechanism and enantioselectivity.
Authors: Liao, L.J. / Zhao, Y.C.
History
DepositionDec 9, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Water


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

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Experimental details

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Experiment

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

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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

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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

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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

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