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- PDB-2vne: The X-ray structure of Norcoclaurine synthase from Thalictrum flavum -

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Basic information

Entry
Database: PDB / ID: 2vne
TitleThe X-ray structure of Norcoclaurine synthase from Thalictrum flavum
ComponentsS-NORCOCLAURINE SYNTHASE
KeywordsLYASE / NORCOCLAURINE SYNTHASE / BIOSYNTHESIS OF BENZYLISOQUINOLINE ALKALOIDS
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
S-norcoclaurine synthase
Similarity search - Component
Biological speciesTHALICTRUM FLAVUM (yellow meadow-rue)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 Å
AuthorsIlari, A. / Franceschini, S. / Boffi, A. / Bonamore, A. / Pasquo, A.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structural Basis of Enzymatic S-Norcoclaurine Biosynthesis.
Authors: Ilari, A. / Franceschini, S. / Bonamore, A. / Arenghi, F. / Botta, B. / Macone, A. / Pasquo, A. / Bellucci, L. / Boffi, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Cloning, Expression, Crystallization and Preliminary X-Ray Data Analysis of Norcoclaurine Synthase from Thalictrum Flavum.
Authors: Pasquo, A. / Bonamore, A. / Franceschini, S. / Macone, A. / Boffi, A. / Ilari, A.
History
DepositionFeb 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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)45,2122
Polymers45,2122
Non-polymers00
Water32418
1
A: S-NORCOCLAURINE SYNTHASE
B: S-NORCOCLAURINE SYNTHASE

A: S-NORCOCLAURINE SYNTHASE
B: S-NORCOCLAURINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)90,4254
Polymers90,4254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area11710 Å2
ΔGint-32.4 kcal/mol
Surface area38960 Å2
MethodPQS
Unit cell
Length a, b, c (Å)86.312, 86.312, 118.361
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein S-NORCOCLAURINE SYNTHASE / NORCOCLAURINE SYNTHASE FROM THALICTRUM FLAVUM


Mass: 22606.209 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-210 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN LACKS THE FIRST 15 RESIDUES AND IS HIS-TAGGED AT THE C-TERMINUS.
Source: (gene. exp.) THALICTRUM FLAVUM (yellow meadow-rue) / Plasmid: PET22-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q67A25, (S)-norcoclaurine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 16 TO MSE ENGINEERED RESIDUE IN CHAIN A, ILE 17 TO THR ...ENGINEERED RESIDUE IN CHAIN A, THR 16 TO MSE ENGINEERED RESIDUE IN CHAIN A, ILE 17 TO THR ENGINEERED RESIDUE IN CHAIN A, ASN 18 TO GLY ENGINEERED RESIDUE IN CHAIN A, CYS 19 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 16 TO MSE ENGINEERED RESIDUE IN CHAIN B, ILE 17 TO THR ENGINEERED RESIDUE IN CHAIN B, ASN 18 TO GLY ENGINEERED RESIDUE IN CHAIN B, CYS 19 TO SER
Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 64.83 % / Description: NONE
Crystal growpH: 4.5
Details: AMMONIUM SULPHATE 0.8-1.3 M, SODIUM CHLORIDE 0.1-0.3 M, ACETATE BUFFER 0.1 M AT PH=4.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13618 / % possible obs: 96 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.72→74.74 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.891 / SU B: 13.867 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.674 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28482 676 5 %RANDOM
Rwork0.23939 ---
obs0.24167 12882 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å20 Å2
2---0.36 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.72→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 0 18 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222624
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9683568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8635325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81725.05101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.66515453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.903153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021917
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21066
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21696
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5071.51671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82622656
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.02631077
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5984.5912
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.49 43
Rwork0.337 898

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