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- PDB-1chw: CHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH HEXANOYL-COA -

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Basic information

Entry
Database: PDB / ID: 1chw
TitleCHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH HEXANOYL-COA
ComponentsPROTEIN (CHALCONE 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
HEXANOYL-COENZYME A / Chalcone synthase 2
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsFerrer, J.-L. / Jez, J. / Bowman, M.E. / 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
DepositionMar 30, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: 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 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 9, 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: PROTEIN (CHALCONE SYNTHASE)
B: PROTEIN (CHALCONE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2104
Polymers85,4782
Non-polymers1,7312
Water7,927440
1
A: PROTEIN (CHALCONE SYNTHASE)
hetero molecules

B: PROTEIN (CHALCONE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2104
Polymers85,4782
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
Buried area8550 Å2
ΔGint-40 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.814, 97.814, 130.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.51134, 0.85938, -0.00073), (0.85937, 0.51133, -0.00389), (-0.00297, -0.00262, -0.99999)
Vector: 0.05599, 0.28936, 195.62721)

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Components

#1: Protein PROTEIN (CHALCONE SYNTHASE) / CHS


Mass: 42739.219 Da / Num. of mol.: 2 / Mutation: C164S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / References: UniProt: P30074, chalcone synthase
#2: Chemical ChemComp-HXC / HEXANOYL-COENZYME A


Mass: 865.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsOTHER CONFORMATION FOR HEXANOYL-COA (THE HEXANOYL PART DOES NOT APPEAR IN THE DENSITY)

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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: THE CRYSTALS WERE OBTAINED OVERNIGHT AT 4 C HANGING-DROP VAPOR DIFFUSION METHOD. THE DROPLET CONSISTED ON 25 MGR/ML (FINAL CONCENTRATION) PROTEIN MIXED WITH THE RESERVOIR WHICH CONTAINED 2.4 ...Details: THE CRYSTALS WERE OBTAINED OVERNIGHT AT 4 C HANGING-DROP VAPOR DIFFUSION METHOD. THE DROPLET CONSISTED ON 25 MGR/ML (FINAL CONCENTRATION) PROTEIN MIXED WITH THE RESERVOIR WHICH CONTAINED 2.4 M AMMONIUM SULFATE, 100 MM PIPES BUFFER (PH 6.5), IN THE PRESENCE (UP TO 5 MM) OR ABSENCE OF DTT REDUCING AGENT. CRYSTALS WERE STABILIZED IN 40% (V/V) PEG400, 100 MM PIPES AND 20 MM HEXANOYL-COA PRIOR TO FREEZING AT 105 K.
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 0.1PIPES1reservoir

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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: Sep 1, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→70.71 Å / Num. obs: 48429 / % possible obs: 84.62 % / Redundancy: 1.81 % / Rsym value: 0.047 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 0.284 % / Mean I/σ(I) obs: 0.95 / Rsym value: 0.18 / % possible all: 23.8
Reflection
*PLUS
Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassification
CCP4(REFMAC+ARPP)model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(ARPP)phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1BI5

1bi5


Resolution: 1.9→70.71 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2421 5 %RANDOM
Rwork0.2129 ---
obs-48429 84.62 %-
Refinement stepCycle: LAST / Resolution: 1.9→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 110 440 6540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d4.086
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor obs: 0.201 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS

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