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- PDB-1cml: CHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH MALONYL-COA -

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Basic information

Entry
Database: PDB / ID: 1cml
TitleCHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH MALONYL-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
MALONYL-COENZYME A / Chalcone synthase 2
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.69 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: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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 1.5Aug 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CHALCONE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9754
Polymers42,7231
Non-polymers1,2523
Water7,188399
1
A: PROTEIN (CHALCONE SYNTHASE)
hetero molecules

A: PROTEIN (CHALCONE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9508
Polymers85,4462
Non-polymers2,5046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area10630 Å2
ΔGint-69 kcal/mol
Surface area26070 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-393-

HOH

21A-417-

HOH

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Components

#1: Protein PROTEIN (CHALCONE SYNTHASE) / CHS


Mass: 42723.219 Da / Num. of mol.: 1 / Mutation: C164A
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-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#4: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAPPEARS DECARBOXYLATED 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: pH 6.50
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / 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: Jul 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: 1.69→84.52 Å / Num. obs: 39507 / % possible obs: 97.3 % / Redundancy: 2.16 % / Rsym value: 0.026 / Net I/σ(I): 15.3
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 7.9 / Rsym value: 0.089 / % possible all: 83.2
Reflection
*PLUS
Highest resolution: 1.69 Å / Lowest resolution: 84.52 Å / % possible obs: 97.3 % / Redundancy: 2.16 % / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
Highest resolution: 1.69 Å / Lowest resolution: 1.73 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 7.9

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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: 1.69→84.52 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1975 5 %RANDOM
Rwork0.1667 ---
obs-39507 97.4 %-
Refinement stepCycle: LAST / Resolution: 1.69→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 77 399 3470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d2.141
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: 1.69 Å / Lowest resolution: 84.52 Å / Rfactor obs: 0.177 / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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