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- PDB-6rp3: Truncated Norcoclaurine synthase with reaction intermediate mimic -

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Basic information

Entry
Database: PDB / ID: 6rp3
TitleTruncated Norcoclaurine synthase with reaction intermediate mimic
ComponentsS-norcoclaurine synthase
KeywordsLYASE / tetrahydroisoquinoline synthase / biotransformation
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 domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KCZ / S-norcoclaurine synthase
Similarity search - Component
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKeep, N.H. / Roddan, R. / Sula, A.
Citation
Journal: Acs Catalysis / Year: 2019
Title: Acceptance and Kinetic Resolution of alpha-Methyl-Substituted Aldehydes by Norcoclaurine Synthases
Authors: Roddan, R. / Gygli, G. / Sula, A. / Lichman, B.R. / Pleiss, J. / Ward, J.M. / Keep, N.H. / Hailes, H.C.
#1: Journal: Biochemistry / Year: 2017
Title: Structural Evidence for the Dopamine-First Mechanism of Norcoclaurine Synthase.
Authors: Lichman, B.R. / Sula, A. / Pesnot, T. / Hailes, H.C. / Ward, J.M. / Keep, N.H.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-norcoclaurine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6965
Polymers18,2381
Non-polymers4584
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint6 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.256, 62.256, 73.579
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein S-norcoclaurine synthase


Mass: 18238.064 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 BL21(DE3) (bacteria) / References: UniProt: Q67A25, (S)-norcoclaurine synthase
#2: Chemical ChemComp-KCZ / 4-[2-[[(2~{R})-2-phenylpropyl]amino]ethyl]benzene-1,2-diol


Mass: 271.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% polyethylene glycol monomethylether 5000, 80 mM Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.81→43.5 Å / Num. obs: 15507 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Net I/σ(I): 10.14
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 2.045 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1116 / CC1/2: 0.642 / Rpim(I) all: 0.864 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8Q

5n8q


Resolution: 1.81→43.49 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.953 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 763 4.9 %RANDOM
Rwork0.1942 ---
obs0.1967 14703 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.18 Å2 / Biso mean: 46.437 Å2 / Biso min: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 1.81→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 32 44 1325
Biso mean--55.76 44.81 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131329
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171266
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.6441806
X-RAY DIFFRACTIONr_angle_other_deg1.4051.5732949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39524.90251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0915224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.839151
X-RAY DIFFRACTIONr_chiral_restr0.0960.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021439
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
LS refinement shellResolution: 1.81→1.856 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.354 39 -
Rwork0.304 1062 -
obs--97.43 %
Refinement TLS params.Method: refined / Origin x: 1.479 Å / Origin y: -20.377 Å / Origin z: 6.995 Å
111213212223313233
T0.0344 Å2-0.0074 Å2-0.0157 Å2-0.2692 Å2-0.0855 Å2--0.0522 Å2
L2.2556 °2-0.81 °2-1.2876 °2-1.7119 °2-0.0993 °2--4.3687 °2
S-0.0809 Å °-0.5207 Å °0.1934 Å °0.1543 Å °0.2485 Å °-0.2691 Å °-0.0712 Å °0.8907 Å °-0.1677 Å °

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