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- PDB-7vez: Crystal structure of Cyclosorus parasiticus chalcone synthase 1 (... -

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Basic information

Entry
Database: PDB / ID: 7vez
TitleCrystal structure of Cyclosorus parasiticus chalcone synthase 1 (CpCHS1) complex with naringenin
Componentschalcone synthases 1
KeywordsTRANSFERASE / flavonoids biosynthesis / chalcone synthase / Cyclosorus parasiticus / naringenin
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / NARINGENIN
Function and homology information
Biological speciesCyclosorus parasiticus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å
AuthorsLi, J.X. / Cheng, A.X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770330 China
National Natural Science Foundation of China (NSFC)32000228 China
National Natural Science Foundation of China (NSFC)31870720 China
CitationJournal: Front Plant Sci / Year: 2021
Title: Functional and Structural Investigation of Chalcone Synthases Based on Integrated Metabolomics and Transcriptome Analysis on Flavonoids and Anthocyanins Biosynthesis of the Fern Cyclosorus parasiticus .
Authors: Niu, M. / Fu, J. / Ni, R. / Xiong, R.L. / Zhu, T.T. / Lou, H.X. / Zhang, P. / Li, J. / Cheng, A.X.
History
DepositionSep 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chalcone synthases 1
B: chalcone synthases 1
C: chalcone synthases 1
D: chalcone synthases 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,4618
Polymers177,3724
Non-polymers1,0894
Water1,892105
1
A: chalcone synthases 1
D: chalcone synthases 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2304
Polymers88,6862
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-23 kcal/mol
Surface area26170 Å2
MethodPISA
2
B: chalcone synthases 1
C: chalcone synthases 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2304
Polymers88,6862
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-20 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.259, 82.289, 134.312
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
chalcone synthases 1


Mass: 44342.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyclosorus parasiticus (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE NCBI ACCESSION NUMBER IS OK136250 FOR THE PROTEIN.

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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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M sodium chloride, 0.1 M Tris-HCl, 20 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.397→30.431 Å / Num. obs: 79991 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.992 / Net I/σ(I): 13.17
Reflection shellResolution: 2.397→2.483 Å / Num. unique obs: 4711 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DXB

6dxb


Resolution: 2.397→30.431 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2729 3.41 %
Rwork0.1803 77262 -
obs0.1821 79991 66.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.63 Å2 / Biso mean: 8.8758 Å2 / Biso min: 0.75 Å2
Refinement stepCycle: final / Resolution: 2.397→30.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12039 0 80 105 12224
Biso mean--9.46 11.26 -
Num. residues----1564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412391
X-RAY DIFFRACTIONf_angle_d1.25416798
X-RAY DIFFRACTIONf_chiral_restr0.0781883
X-RAY DIFFRACTIONf_plane_restr0.012148
X-RAY DIFFRACTIONf_dihedral_angle_d21.984536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.397-2.44050.3393800.2735224236
2.4405-2.48740.3242910.2843258442
2.4874-2.53820.3692920.2796258143
2.5382-2.59330.332980.2691278645
2.5933-2.65360.3286990.2839286047
2.6536-2.71990.3121040.2831298949
2.7199-2.79340.29321120.2825319252
2.7934-2.87560.32991190.2705332355
2.8756-2.96830.29991290.2523353458
2.9683-3.07430.27511330.2369374462
3.0743-3.19730.29061460.2193407166
3.1973-3.34260.27521460.2096428871
3.3426-3.51860.23981690.184473978
3.5186-3.73870.22691820.1691513784
3.7387-4.02670.20041840.16528787
4.0267-4.43090.20972000.1374580696
4.4309-5.06950.172160.1329606199
5.0695-6.37730.22112140.1595605999
6.3773-30.4310.16612150.1419597998

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