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- PDB-2vq5: X-ray structure of Norcoclaurine synthase from Thalictrum flavum ... -

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Basic information

Entry
Database: PDB / ID: 2vq5
TitleX-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde
ComponentsS-NORCOCLAURINE SYNTHASE
KeywordsLYASE / NORCOCLAURINE SYNTHASE / S- NORCOCLAURINE BIOSYNTHESIS / DOPAMINE / HYDROXYBENZALDEHYDE
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
ACETATE ION / P-HYDROXYBENZALDEHYDE / L-DOPAMINE / S-norcoclaurine synthase
Similarity search - Component
Biological speciesTHALICTRUM FLAVUM (yellow meadow-rue)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsIlari, A. / Franceschini, S. / Bonamore, A. / Boffi, A.
CitationJournal: 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.
History
DepositionMar 11, 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,90512
Polymers45,2122
Non-polymers69310
Water3,117173
1
A: S-NORCOCLAURINE SYNTHASE
B: S-NORCOCLAURINE SYNTHASE
hetero molecules

A: S-NORCOCLAURINE SYNTHASE
B: S-NORCOCLAURINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,81024
Polymers90,4254
Non-polymers1,38620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area12410 Å2
ΔGint-39 kcal/mol
Surface area38240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)86.474, 86.474, 117.977
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 183 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical ChemComp-LDP / L-DOPAMINE / DOPAMINE


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2 / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

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
Sequence detailsDATABASE NAME NCBI THE PROTEIN HAS SIX HIS AT THE C- TERMINUS AND LACKS THE FIRST 15 RESIDUES

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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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 4.5
Details: AMMONIUM SULFATE 1.4-1.8 M, NACL 0.2 M, ACETATE BUFFER PH 4.0-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 30118 / % possible obs: 97.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VNE

2vne


Resolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.069 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26605 1508 5 %RANDOM
Rwork0.22086 ---
obs0.22312 28573 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.381 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 42 173 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222691
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9893654
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2385333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63925.15299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79315468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.218153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021970
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21232
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21766
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8161.51720
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30422695
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8431130
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7544.5957
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: 2.089→2.144 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 99
Rwork0.265 2045

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