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- PDB-1bq6: CHALCONE SYNTHASE FROM ALFALFA WITH COENZYME A -

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Basic information

Entry
Database: PDB / ID: 1bq6
TitleCHALCONE SYNTHASE FROM ALFALFA WITH COENZYME A
ComponentsCHALCONE SYNTHASE
KeywordsTRANSFERASE / POLYKETIDE SYNTHASE / CHALCONE BIOSYNTHESIS
Function / homology
Function and homology information


chalcone biosynthetic process / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / 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 ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / 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
COENZYME A / Chalcone synthase 2
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.56 Å
AuthorsFerrer, J.-L. / Bowman, M.E. / Jez, J. / Dixon, R. / 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
DepositionAug 21, 1998Processing site: BNL
Revision 1.0Aug 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHALCONE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5203
Polymers42,6561
Non-polymers8642
Water6,251347
1
A: CHALCONE SYNTHASE
hetero molecules

A: CHALCONE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0396
Polymers85,3122
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area8740 Å2
ΔGint-40 kcal/mol
Surface area26350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.631, 97.631, 65.303
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-394-

HOH

21A-396-

HOH

31A-414-

HOH

41A-621-

HOH

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Components

#1: Protein CHALCONE SYNTHASE / CHS


Mass: 42656.086 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: PT-COATED MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.58→35.5 Å / Num. obs: 45366 / % possible obs: 91.5 % / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 23.8
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.191 / % possible all: 69.6

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1BI5

1bi5


Resolution: 1.56→10 Å / Num. parameters: 31993 / Num. restraintsaints: 40273 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE FIRST STEP OF THE REFINEMENT WAS PERFORMED WITH REFMAC AND ARP. ANISOTROPIC SCALING WAS APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. ANISOTROPIC REFINEMENT ...Details: THE FIRST STEP OF THE REFINEMENT WAS PERFORMED WITH REFMAC AND ARP. ANISOTROPIC SCALING WAS APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.84%
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 2264 5.26 %RANDOM
all0.1678 43012 --
obs0.1654 -87.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3364.6
Refinement stepCycle: LAST / Resolution: 1.56→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 53 347 3389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.048
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.022
X-RAY DIFFRACTIONs_approx_iso_adps0.025
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1654
Solvent computation
*PLUS
Displacement parameters
*PLUS

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