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- PDB-1bi5: CHALCONE SYNTHASE FROM ALFALFA -

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Basic information

Entry
Database: PDB / ID: 1bi5
TitleCHALCONE SYNTHASE FROM ALFALFA
ComponentsCHALCONE SYNTHASE
KeywordsPOLYKETIDE SYNTHASE / CHALCONE BIOSYNTHESIS
Function / homology
Function and homology information


chalcone biosynthetic process / chalcone synthase activity / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / MIRAS, SOLVENT FLIPPING / Resolution: 1.56 Å
AuthorsFerrer, J.L. / Jez, J.M. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis.
Authors: Ferrer, J.L. / Jez, J.M. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
History
DepositionJun 22, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHALCONE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)42,7871
Polymers42,7871
Non-polymers00
Water8,629479
1
A: CHALCONE SYNTHASE

A: CHALCONE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)85,5752
Polymers85,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area6140 Å2
ΔGint-10 kcal/mol
Surface area27150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.540, 97.540, 65.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

21A-460-

HOH

31A-464-

HOH

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Components

#1: Protein CHALCONE SYNTHASE / / CHS


Mass: 42787.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Tissue: 21 DAY OLD ROOT NODULE / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30074, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 42 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
22.2-2.4 Mammonium sulfate1reservoir
30.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.56→25 Å / Num. obs: 46763 / % possible obs: 93.3 % / Redundancy: 5 % / Rsym value: 0.039 / Net I/σ(I): 38.2
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 1 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.163 / % possible all: 62.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
SHELXL-97refinement
RefinementMethod to determine structure: MIRAS, SOLVENT FLIPPING / Resolution: 1.56→10 Å / Num. parameters: 32565 / Num. restraintsaints: 41135 / Cross valid method: RANDOM / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: 1ST STEP OF THE REFINEMENT PERFORMED WITH REFMAC + ARP.
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 2507 5.4 %0.05
all0.1324 46763 --
obs0.1355 -91.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3413.2
Refinement stepCycle: LAST / Resolution: 1.56→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 0 479 3476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.001
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.029
X-RAY DIFFRACTIONs_approx_iso_adps0.028
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1355
Solvent computation
*PLUS
Displacement parameters
*PLUS

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