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- PDB-9c3x: Crystal structure of biphenyl synthase from Malus domestica compl... -

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Basic information

Entry
Database: PDB / ID: 9c3x
TitleCrystal structure of biphenyl synthase from Malus domestica complexed with triketide-CoA mimetic
ComponentsBIS3 biphenyl synthase
KeywordsTRANSFERASE / polyketide synthase / CoA analog
Function / homology
Function and homology information


3,5-dihydroxybiphenyl synthase / biphenyl synthase activity / polyketide biosynthetic process
Similarity search - Function
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-like
Similarity search - Domain/homology
: / (3R)-butane-1,3-diol / BIS3 biphenyl synthase
Similarity search - Component
Biological speciesMalus domestica (apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRe, R.N. / Noel, J.P. / Burkart, M.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM139327 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM095970 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Elucidating the Iterative Elongation Mechanism in a Type III Polyketide Synthase.
Authors: Re, R.N. / La Clair, J.J. / Noel, J.P. / Burkart, M.D.
History
DepositionJun 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIS3 biphenyl synthase
B: BIS3 biphenyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5936
Polymers86,5632
Non-polymers2,0304
Water17,078948
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-24 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.290, 113.250, 63.020
Angle α, β, γ (deg.)90.000, 93.350, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein BIS3 biphenyl synthase


Mass: 43281.641 Da / Num. of mol.: 2 / Mutation: A251V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus domestica (apple) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K9MST3, 3,5-dihydroxybiphenyl synthase
#2: Chemical ChemComp-BU4 / (3R)-butane-1,3-diol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-A1AUA / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-[(3-oxo-3-{[2-(5-oxo-5-phenylpentanamido)ethyl]amino}propyl)amino]butyl dihydrogen diphosphate


Mass: 924.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H47N8O18P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 948 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 14-18% PEG8000, 0.3 M ammonium acetate, 0.1 M sodium HEPES
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.45→55.2 Å / Num. obs: 134619 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 9.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.1
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6524 / CC1/2: 0.573 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLM7.4.0data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→55.2 Å / SU ML: 0.1418 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.6569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1638 6818 5.07 %
Rwork0.1423 127718 -
obs0.1435 134536 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.64 Å2
Refinement stepCycle: LAST / Resolution: 1.45→55.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5911 0 134 948 6993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00846315
X-RAY DIFFRACTIONf_angle_d1.07828589
X-RAY DIFFRACTIONf_chiral_restr0.082961
X-RAY DIFFRACTIONf_plane_restr0.00841102
X-RAY DIFFRACTIONf_dihedral_angle_d9.4979892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.29712250.27394204X-RAY DIFFRACTION97.71
1.47-1.480.30322260.24294143X-RAY DIFFRACTION96.74
1.48-1.50.21971980.22764305X-RAY DIFFRACTION98.82
1.5-1.520.2241970.21574239X-RAY DIFFRACTION99.04
1.52-1.540.21282140.19924348X-RAY DIFFRACTION98.92
1.54-1.560.21942460.20314219X-RAY DIFFRACTION99.11
1.56-1.580.23972000.19514336X-RAY DIFFRACTION98.89
1.58-1.610.2392160.1894210X-RAY DIFFRACTION99.06
1.61-1.630.20792420.19314310X-RAY DIFFRACTION98.7
1.63-1.660.20052150.19154308X-RAY DIFFRACTION98.97
1.66-1.690.21572100.17574210X-RAY DIFFRACTION98.46
1.69-1.720.18782450.16554229X-RAY DIFFRACTION98.46
1.72-1.750.19222280.16334237X-RAY DIFFRACTION98.35
1.75-1.790.1842220.15354230X-RAY DIFFRACTION97.74
1.79-1.830.18112400.14214149X-RAY DIFFRACTION96.46
1.83-1.870.15612400.13734249X-RAY DIFFRACTION99.12
1.87-1.920.16552410.14424299X-RAY DIFFRACTION99.28
1.92-1.970.15972410.14224285X-RAY DIFFRACTION99.21
1.97-2.030.17272280.14444276X-RAY DIFFRACTION99.16
2.03-2.090.15662230.12924273X-RAY DIFFRACTION98.83
2.09-2.170.15062280.12154257X-RAY DIFFRACTION99.07
2.17-2.250.14452470.11794257X-RAY DIFFRACTION98.36
2.25-2.360.14022150.12064207X-RAY DIFFRACTION97.72
2.36-2.480.1692250.11894227X-RAY DIFFRACTION97.29
2.48-2.630.14852180.1214195X-RAY DIFFRACTION96.04
2.63-2.840.13762180.11884288X-RAY DIFFRACTION99.6
2.84-3.120.16172570.12454292X-RAY DIFFRACTION99.58
3.12-3.580.122230.12124338X-RAY DIFFRACTION99.63
3.58-4.50.12722560.11054274X-RAY DIFFRACTION98.14
4.5-55.20.13932340.13784324X-RAY DIFFRACTION98.42

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