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- PDB-5ypt: Crystal structure of Marchantia paleacea chalone synthase like 1 ... -

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Basic information

Entry
Database: PDB / ID: 5ypt
TitleCrystal structure of Marchantia paleacea chalone synthase like 1 (CHSL1)
ComponentsStilbenecarboxylate synthase 1
KeywordsTRANSFERASE / CHALCONE SYNTHASE / PKS TYPE III / CHSL1
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Stilbenecarboxylate synthase 1
Similarity search - Component
Biological speciesMarchantia polymorpha (liverwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsLou, H.X. / Yu, H.
CitationJournal: Plant Physiol. Biochem. / Year: 2018
Title: Structural and biochemical characterization of the plant type III polyketide synthases of the liverwort Marchantia paleacea.
Authors: Yu, H.N. / Liu, X.Y. / Gao, S. / Sun, B. / Zheng, H.B. / Ji, M. / Cheng, A.X. / Lou, H.X.
History
DepositionNov 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Stilbenecarboxylate synthase 1
B: Stilbenecarboxylate synthase 1
C: Stilbenecarboxylate synthase 1
D: Stilbenecarboxylate synthase 1
E: Stilbenecarboxylate synthase 1
F: Stilbenecarboxylate synthase 1


Theoretical massNumber of molelcules
Total (without water)279,5756
Polymers279,5756
Non-polymers00
Water10,485582
1
A: Stilbenecarboxylate synthase 1
B: Stilbenecarboxylate synthase 1


Theoretical massNumber of molelcules
Total (without water)93,1922
Polymers93,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-6 kcal/mol
Surface area26750 Å2
MethodPISA
2
C: Stilbenecarboxylate synthase 1
D: Stilbenecarboxylate synthase 1


Theoretical massNumber of molelcules
Total (without water)93,1922
Polymers93,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-8 kcal/mol
Surface area26660 Å2
MethodPISA
3
E: Stilbenecarboxylate synthase 1
F: Stilbenecarboxylate synthase 1


Theoretical massNumber of molelcules
Total (without water)93,1922
Polymers93,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-8 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.183, 74.581, 262.155
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASPchain A and (resid 15:253 or resid 255:266 or resid 272:393 )AA15 - 25351 - 289
12ALAALAILEILEchain A and (resid 15:253 or resid 255:266 or resid 272:393 )AA255 - 266291 - 302
13ASPASPHISHISchain A and (resid 15:253 or resid 255:266 or resid 272:393 )AA272 - 393308 - 429
21ALAALAASPASPchain B and (resid 15:253 or resid 255:266 or resid 272:393 )BB15 - 25351 - 289
22ALAALAILEILEchain B and (resid 15:253 or resid 255:266 or resid 272:393 )BB255 - 266291 - 302
23ASPASPHISHISchain B and (resid 15:253 or resid 255:266 or resid 272:393 )BB272 - 393308 - 429
31ALAALAASPASPchain C and (resid 15:253 or resid 255:266 or resid 272:393 )CC15 - 25351 - 289
32ALAALAILEILEchain C and (resid 15:253 or resid 255:266 or resid 272:393 )CC255 - 266291 - 302
33ASPASPHISHISchain C and (resid 15:253 or resid 255:266 or resid 272:393 )CC272 - 393308 - 429
41ALAALAASPASPchain D and (resid 15:253 or resid 255:266 or resid 272:393 )DD15 - 25351 - 289
42ALAALAILEILEchain D and (resid 15:253 or resid 255:266 or resid 272:393 )DD255 - 266291 - 302
43ASPASPHISHISchain D and (resid 15:253 or resid 255:266 or resid 272:393 )DD272 - 393308 - 429
51ALAALAASPASPchain E and (resid 15:253 or resid 255:266 or resid 272:393 )EE15 - 25351 - 289
52ALAALAILEILEchain E and (resid 15:253 or resid 255:266 or resid 272:393 )EE255 - 266291 - 302
53ASPASPHISHISchain E and (resid 15:253 or resid 255:266 or resid 272:393 )EE272 - 393308 - 429
61ALAALAASPASPchain F and (resid 15:253 or resid 255:266 or resid 272:393 )FF15 - 25351 - 289
62ALAALAILEILEchain F and (resid 15:253 or resid 255:266 or resid 272:393 )FF255 - 266291 - 302
63ASPASPHISHISchain F and (resid 15:253 or resid 255:266 or resid 272:393 )FF272 - 393308 - 429

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Components

#1: Protein
Stilbenecarboxylate synthase 1


Mass: 46595.859 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marchantia polymorpha (liverwort) / Gene: STCS1 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5I6Y2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 0.2 M ammonium sulfate, 0.1 M BIS-TRIS buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.394→50 Å / Num. obs: 93629 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 13.7
Reflection shellResolution: 2.394→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.9 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P0U

2p0u


Resolution: 2.394→48.247 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 4701 5.02 %Random
Rwork0.194 ---
obs0.1967 93591 98.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 2.394→48.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17682 0 0 582 18264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918065
X-RAY DIFFRACTIONf_angle_d1.26324542
X-RAY DIFFRACTIONf_dihedral_angle_d14.2036634
X-RAY DIFFRACTIONf_chiral_restr0.0522809
X-RAY DIFFRACTIONf_plane_restr0.0073188
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13CX-RAY DIFFRACTIONPOSITIONAL
14DX-RAY DIFFRACTIONPOSITIONAL
15EX-RAY DIFFRACTIONPOSITIONAL
16FX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3936-2.42080.35091140.25992364X-RAY DIFFRACTION81
2.4208-2.44920.30051300.24742775X-RAY DIFFRACTION92
2.4492-2.47910.29371510.23472924X-RAY DIFFRACTION95
2.4791-2.51050.29171520.23442817X-RAY DIFFRACTION98
2.5105-2.54350.30161420.23743027X-RAY DIFFRACTION99
2.5435-2.57840.30911600.24672993X-RAY DIFFRACTION100
2.5784-2.61520.32161340.24422977X-RAY DIFFRACTION100
2.6152-2.65420.33031670.24062997X-RAY DIFFRACTION99
2.6542-2.69570.31961630.22062926X-RAY DIFFRACTION100
2.6957-2.73990.29751560.22663052X-RAY DIFFRACTION100
2.7399-2.78710.27161540.22482935X-RAY DIFFRACTION100
2.7871-2.83780.30061710.21722994X-RAY DIFFRACTION100
2.8378-2.89240.31511560.22862959X-RAY DIFFRACTION100
2.8924-2.95140.30111520.21423011X-RAY DIFFRACTION100
2.9514-3.01560.2881630.21552961X-RAY DIFFRACTION100
3.0156-3.08570.27611720.22013052X-RAY DIFFRACTION100
3.0857-3.16290.26471710.21332897X-RAY DIFFRACTION100
3.1629-3.24840.24821560.21143051X-RAY DIFFRACTION100
3.2484-3.34390.26071720.20522942X-RAY DIFFRACTION100
3.3439-3.45180.25491860.20572971X-RAY DIFFRACTION100
3.4518-3.57520.28131450.19833033X-RAY DIFFRACTION100
3.5752-3.71830.22671760.18742994X-RAY DIFFRACTION100
3.7183-3.88740.2281390.17823005X-RAY DIFFRACTION99
3.8874-4.09230.19541580.16173013X-RAY DIFFRACTION99
4.0923-4.34850.19851610.16162990X-RAY DIFFRACTION99
4.3485-4.6840.22731690.15573012X-RAY DIFFRACTION99
4.684-5.15490.21011500.1593017X-RAY DIFFRACTION100
5.1549-5.89970.19961510.18373022X-RAY DIFFRACTION99
5.8997-7.42860.26051560.19313098X-RAY DIFFRACTION100
7.4286-48.25670.1881740.15563081X-RAY DIFFRACTION98

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