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- PDB-5n8q: Structure of truncated Norcoclaurine Synthase from Thalictrum flavum -

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Basic information

Entry
Database: PDB / ID: 5n8q
TitleStructure of truncated Norcoclaurine Synthase from Thalictrum flavum
ComponentsS-norcoclaurine synthase
KeywordsLYASE / Pictet Spengler condensation / Dopamine
Function / homology
Function and homology information


(S)-norcoclaurine synthase / (S)-norcoclaurine synthase activity / alkaloid metabolic process / defense response
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 subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSula, A. / Lichman, B.R. / Pesnot, T. / Ward, J.M. / Hailes, H.C. / Keep, N.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust096626/Z/11/Z United Kingdom
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
DepositionFeb 24, 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 1.2Jan 17, 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 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,7143
Polymers54,7143
Non-polymers00
Water7,782432
1
A: S-norcoclaurine synthase


Theoretical massNumber of molelcules
Total (without water)18,2381
Polymers18,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-norcoclaurine synthase


Theoretical massNumber of molelcules
Total (without water)18,2381
Polymers18,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: S-norcoclaurine synthase


Theoretical massNumber of molelcules
Total (without water)18,2381
Polymers18,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.046, 109.632, 136.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-325-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 38 - 194 / Label seq-ID: 7 - 163

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% w/v polyethylene glycol 1000, 10% w/v polyethylene glycol 8000 20 mM Tris, 50 mM NaCl, ph 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→109.63 Å / Num. obs: 39359 / % possible obs: 99.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 27.34 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.141 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALS1.0-0-g66ac5d4data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VQ5 CHAIN A

2vq5


Resolution: 2→85.68 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.687 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1960 5 %RANDOM
Rwork0.197 ---
obs0.199 37264 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2→85.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 0 432 4135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193810
X-RAY DIFFRACTIONr_bond_other_d0.0020.023600
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.9645191
X-RAY DIFFRACTIONr_angle_other_deg1.05838378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04925.205146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75415641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.761153
X-RAY DIFFRACTIONr_chiral_restr0.1320.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
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_it1.6621.7521907
X-RAY DIFFRACTIONr_mcbond_other1.6521.7511906
X-RAY DIFFRACTIONr_mcangle_it2.6432.6112379
X-RAY DIFFRACTIONr_mcangle_other2.6442.6132380
X-RAY DIFFRACTIONr_scbond_it2.0581.9981903
X-RAY DIFFRACTIONr_scbond_other2.0571.9991904
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2382.9052812
X-RAY DIFFRACTIONr_long_range_B_refined6.82422.9424293
X-RAY DIFFRACTIONr_long_range_B_other6.68621.7834163
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)
11A94880.08
12B94880.08
21A94080.1
22C94080.1
31B94300.1
32C94300.1
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 129 -
Rwork0.259 2705 -
obs--99.68 %
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)
11.73110.10941.93781.75220.79242.43920.1143-0.01170.0682-0.1056-0.24890.09710.0474-0.08580.13460.2164-0.0395-0.0340.1096-0.00570.0674-17.597-11.48719.014
20.39180.11790.88222.0373-0.90032.6799-0.02310.0194-0.0210.3150.0691-0.0166-0.2033-0.0303-0.0460.3436-0.039-0.02280.09820.00420.0029-0.9196.21548.237
30.1021-0.1911-0.33661.2454-0.02962.79140.04660.0025-0.039-0.032-0.0898-0.0968-0.32540.04040.04320.2805-0.0209-0.01080.08470.00730.08610.18323.22114.893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 195
2X-RAY DIFFRACTION2B38 - 195
3X-RAY DIFFRACTION3C38 - 196

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