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- PDB-9c3w: Crystal structure of biphenyl synthase from Malus domestica compl... -

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Basic information

Entry
Database: PDB / ID: 9c3w
TitleCrystal structure of biphenyl synthase from Malus domestica complexed with diketide-CoA mimetics
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: 1.57 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)88,5816
Polymers86,5632
Non-polymers2,0184
Water14,934829
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-11 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.250, 112.520, 62.710
Angle α, β, γ (deg.)90.000, 93.340, 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-A1AT9 / [(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-[2-(2-phenyl-1,3-dioxolan-2-yl)acetamido]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate


Mass: 940.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H47N8O19P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1AT8 / [(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-(3-oxo-3-phenylpropanamido)ethyl]amino}propyl)amino]butyl dihydrogen diphosphate


Mass: 896.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H43N8O18P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
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: 8.2.2 / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 12, 2022
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.57→56.26 Å / Num. obs: 105231 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 9.82 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5024 / CC1/2: 0.857 / % possible all: 96.6

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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: 1.57→56.26 Å / SU ML: 0.1461 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.4029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1729 5126 4.87 %
Rwork0.1428 100050 -
obs0.1443 105176 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 1.57→56.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5911 0 133 829 6873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00946292
X-RAY DIFFRACTIONf_angle_d1.10438555
X-RAY DIFFRACTIONf_chiral_restr0.0633956
X-RAY DIFFRACTIONf_plane_restr0.00891097
X-RAY DIFFRACTIONf_dihedral_angle_d9.4596887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.24011460.22133280X-RAY DIFFRACTION96.51
1.59-1.610.2471660.21233233X-RAY DIFFRACTION96.23
1.61-1.630.27411850.20123280X-RAY DIFFRACTION97.63
1.63-1.650.22171670.19083227X-RAY DIFFRACTION97.03
1.65-1.670.19421660.17513285X-RAY DIFFRACTION97.62
1.67-1.690.20651760.16953265X-RAY DIFFRACTION97.15
1.69-1.720.17191420.16783317X-RAY DIFFRACTION97.91
1.72-1.740.20471510.1713285X-RAY DIFFRACTION96.95
1.74-1.770.19581580.16663262X-RAY DIFFRACTION97.13
1.77-1.80.17891840.16053307X-RAY DIFFRACTION98.17
1.8-1.830.19181750.15013315X-RAY DIFFRACTION99.37
1.83-1.860.18011770.14823332X-RAY DIFFRACTION99.41
1.86-1.90.1991580.15763401X-RAY DIFFRACTION99.66
1.9-1.940.1991660.1673331X-RAY DIFFRACTION99.6
1.94-1.980.19861630.15733408X-RAY DIFFRACTION99.55
1.98-2.020.17061730.13593345X-RAY DIFFRACTION99.83
2.02-2.070.16611620.13593355X-RAY DIFFRACTION99.8
2.07-2.130.16521620.1333397X-RAY DIFFRACTION99.75
2.13-2.190.15991510.12653370X-RAY DIFFRACTION99.69
2.19-2.260.14931600.13173357X-RAY DIFFRACTION99.74
2.26-2.350.13941730.12633359X-RAY DIFFRACTION99.8
2.35-2.440.14791790.12773365X-RAY DIFFRACTION99.38
2.44-2.550.18031710.12833340X-RAY DIFFRACTION99.15
2.55-2.680.16061950.13093348X-RAY DIFFRACTION99.75
2.68-2.850.16412010.1283375X-RAY DIFFRACTION99.8
2.85-3.070.15811770.133359X-RAY DIFFRACTION99.8
3.07-3.380.15181780.12683379X-RAY DIFFRACTION99.86
3.38-3.870.16272160.1253349X-RAY DIFFRACTION99.94
3.87-4.880.13541860.11773360X-RAY DIFFRACTION99.36
4.88-56.260.20651620.16913464X-RAY DIFFRACTION99.92

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