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- PDB-1d6f: CHALCONE SYNTHASE C164A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1d6f
TitleCHALCONE SYNTHASE C164A MUTANT
ComponentsCHALCONE SYNTHASE
KeywordsTRANSFERASE / POLYPETIDE SYNTHASE / FLAVONOID BIOSYNTHESIS / MALONYL-COA DECARBOXYLATION / SITE- DIRECTED MUTANT
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 / Resolution: 1.69 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_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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)43,1023
Polymers42,7231
Non-polymers3782
Water6,557364
1
A: CHALCONE SYNTHASE
hetero molecules

A: CHALCONE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2036
Polymers85,4462
Non-polymers7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area7730 Å2
ΔGint-35 kcal/mol
Surface area27080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.768, 97.768, 65.228
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-392-

HOH

21A-409-

HOH

31A-458-

HOH

41A-755-

HOH

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Components

#1: Protein CHALCONE SYNTHASE /


Mass: 42723.219 Da / Num. of mol.: 1 / Mutation: C164A
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
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
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
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, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→25 Å / Num. all: 88359 / Num. obs: 39526 / % possible obs: 97 % / Redundancy: 2.2 % / Biso Wilson estimate: 17.48 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 18.8
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 2 % / Rmerge(I) obs: 0.089 / % possible all: 83.2
Reflection
*PLUS
Num. measured all: 88359
Reflection shell
*PLUS
% possible obs: 83.2 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementResolution: 1.69→24.45 Å / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.201 1984 RANDOM
Rwork0.182 --
all0.171 40594 -
obs-39523 -
Refinement stepCycle: LAST / Resolution: 1.69→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 24 364 3382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1
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 Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_deg2.1

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