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- PDB-5non: Structure of truncated Norcoclaurine Synthase from Thalictrum fla... -

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Basic information

Entry
Database: PDB / ID: 5non
TitleStructure of truncated Norcoclaurine Synthase from Thalictrum flavum with product mimic
ComponentsS-norcoclaurine synthase
KeywordsLYASE / Pictet Spengler condensation / Dopamine
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-93H / S-norcoclaurine synthase
Similarity search - Component
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsSula, A. / Lichman, B.R. / Pesnot, T. / Ward, J.M. / Hailes, H.C. / Keep, N.H.
CitationJournal: 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
DepositionApr 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-norcoclaurine synthase
B: S-norcoclaurine synthase
C: S-norcoclaurine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5766
Polymers54,7143
Non-polymers8623
Water8,053447
1
A: S-norcoclaurine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5252
Polymers18,2381
Non-polymers2871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-norcoclaurine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5252
Polymers18,2381
Non-polymers2871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: S-norcoclaurine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5252
Polymers18,2381
Non-polymers2871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.310, 110.218, 136.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA40 - 1939 - 162
21SERSERGLUGLUBB40 - 1939 - 162
12SERSERGLUGLUAA40 - 1939 - 162
22SERSERGLUGLUCC40 - 1939 - 162
13VALVALHISHISBB39 - 1948 - 163
23VALVALHISHISCC39 - 1948 - 163

NCS ensembles :
ID
1
2
3

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Components

#1: Protein S-norcoclaurine synthase


Mass: 18238.064 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant)
Plasmid: PD451 - SR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q67A25, (S)-norcoclaurine synthase
#2: Chemical ChemComp-93H / 4-[2-[2-(4-methoxyphenyl)ethylamino]ethyl]benzene-1,2-diol


Mass: 287.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 10% W/V POLYETHYLENE GLYCOL 1000, 10% REMARK 280 W/V POLYETHYLENE GLYCOL 8000 20 MM TRIS, 50 MM NACL, PH 7.5, PH REMARK 280 8.5, 10 mM Ligand

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→85.85 Å / Num. obs: 50659 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.032 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3072 / Rpim(I) all: 0.35 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALS1.1.3data reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 1.85→86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.774 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22351 2535 5 %RANDOM
Rwork0.18693 ---
obs0.1888 48057 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-0 Å2
2---1.61 Å20 Å2
3---2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.85→86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 63 447 4170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0193917
X-RAY DIFFRACTIONr_bond_other_d0.0020.023718
X-RAY DIFFRACTIONr_angle_refined_deg2.7931.9585325
X-RAY DIFFRACTIONr_angle_other_deg1.30438646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98225.241145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10215651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.124153
X-RAY DIFFRACTIONr_chiral_restr0.1970.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0214661
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02731
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.491.1071887
X-RAY DIFFRACTIONr_mcbond_other1.4791.1061886
X-RAY DIFFRACTIONr_mcangle_it2.2951.6462356
X-RAY DIFFRACTIONr_mcangle_other2.2961.6472357
X-RAY DIFFRACTIONr_scbond_it1.9851.3912030
X-RAY DIFFRACTIONr_scbond_other1.9851.3932031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0691.9942965
X-RAY DIFFRACTIONr_long_range_B_refined5.04514.2974327
X-RAY DIFFRACTIONr_long_range_B_other5.04514.3014328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95060.08
12B95060.08
21A94440.08
22C94440.08
31B95720.09
32C95720.09
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 205 -
Rwork0.267 3496 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2227-0.12591.44171.61450.20332.22520.08880.089-0.1013-0.1193-0.04590.0347-0.001-0.0178-0.04290.3126-0.0141-0.02720.25140.01030.0298-16.615-11.13719.087
21.38590.02821.28572.2905-1.0733.6834-0.0004-0.15850.05230.37070.0104-0.0125-0.2471-0.0671-0.010.3857-0.02340.00950.30370.00010.0048-1.4736.0748.112
30.8382-0.1739-0.42141.89430.76643.23960.07070.03620.1064-0.0992-0.0773-0.1607-0.16220.040.00660.3143-0.0288-0.0010.27330.00250.04380.523.2915.137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 501
2X-RAY DIFFRACTION2B38 - 501
3X-RAY DIFFRACTION3C39 - 501

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