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- PDB-1d6h: CHALONE SYNTHASE (N336A MUTANT COMPLEXED WITH COA) -

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Basic information

Entry
Database: PDB / ID: 1d6h
TitleCHALONE SYNTHASE (N336A MUTANT COMPLEXED WITH COA)
ComponentsCHALCONE SYNTHASE
KeywordsTRANSFERASE / POLYPETIDE SYNTHASE / FLAVONOID BIOSYNTHESIS / MALONYL-COA DECARBOXYLATION / SITE-DIRECTED MUTANT
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 / Resolution: 2.15 Å
AuthorsJez, J.M. / Ferrer, J.L. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
CitationJournal: Biochemistry / Year: 2000
Title: Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase.
Authors: Jez, J.M. / Ferrer, J.L. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
History
DepositionOct 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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

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Assembly

Deposited unit
A: CHALCONE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3783
Polymers42,5141
Non-polymers8642
Water3,315184
1
A: CHALCONE SYNTHASE
hetero molecules

A: CHALCONE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7556
Polymers85,0282
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area8440 Å2
ΔGint-37 kcal/mol
Surface area26550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.361, 97.361, 65.207
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-397-

HOH

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Components

#1: Protein CHALCONE SYNTHASE


Mass: 42513.934 Da / Num. of mol.: 1 / Mutation: N336A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Production host: Escherichia coli (E. coli) / 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.: 184 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.2-2.4 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, 2 MM DITHIOTHREITOL (DTT), pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2-2.4 Mammonium sulfate1reservoir
20.1 Mbis-Tris-propane1reservoir
32 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→21 Å / Num. all: 49636 / Num. obs: 18202 / % possible obs: 91.9 % / Redundancy: 2.72 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.1
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.303 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 49636
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementResolution: 2.15→85 Å / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.25744 932 RANDOM
Rwork0.18425 --
all0.17964 49636 -
obs-17210 -
Refinement stepCycle: LAST / Resolution: 2.15→85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 53 184 3216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3
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
Rfactor Rfree: 0.257 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.015

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