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- PDB-5wc4: Crystal structure of biphenyl synthase from Malus domestic comple... -

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Basic information

Entry
Database: PDB / ID: 5wc4
TitleCrystal structure of biphenyl synthase from Malus domestic complexed with benzoyl-CoA
ComponentsBIS3 biphenyl synthase
KeywordsTRANSFERASE / thiolase fold / polyketide synthase
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/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(3R)-butane-1,3-diol / benzoyl coenzyme A / BIS3 biphenyl synthase
Similarity search - Component
Biological speciesMalus domestica (apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsStewart Jr, C.E. / Noel, J.P.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Molecular architectures of benzoic acid-specific type III polyketide synthases.
Authors: Stewart, C. / Woods, K. / Macias, G. / Allan, A.C. / Hellens, R.P. / Noel, J.P.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 2.0Nov 13, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)88,4316
Polymers86,5072
Non-polymers1,9244
Water18,7541041
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-11 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.247, 112.985, 62.783
Angle α, β, γ (deg.)90.000, 93.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BIS3 biphenyl synthase


Mass: 43253.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus domestica (apple) / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-BYC / benzoyl coenzyme A


Mass: 871.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H40N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1041 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 = protein : Sodium-HEPES (pH7.5) 0.1M, Ammonium Acetate 0.2M, PEG8000 14%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2010 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 239899 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.83 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.443 / Net I/σ(I): 10.6 / Num. measured all: 876363
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.2-1.223.40.4771.4111100
1.22-1.243.50.4181.4011100
1.24-1.273.60.3721.3691100
1.27-1.293.60.331.3471100
1.29-1.323.60.2981.3751100
1.32-1.353.60.2731.2461100
1.35-1.393.60.2311.2171100
1.39-1.423.70.21.1481100
1.42-1.463.70.1731.1941100
1.46-1.513.70.1451.2911100
1.51-1.573.70.1261.4231100
1.57-1.633.70.111.5131100
1.63-1.73.70.0991.648199.9
1.7-1.793.70.0931.6721100
1.79-1.93.70.0821.8321100
1.9-2.053.70.0742.072199.9
2.05-2.263.70.0641.8421100
2.26-2.593.70.0531.6621100
2.59-3.263.80.0441.191199.9
3.26-503.60.0370.951197.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W8Q

5w8q


Resolution: 1.2→42.631 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.36
RfactorNum. reflection% reflection
Rfree0.1247 11955 5.02 %
Rwork0.1001 --
obs0.1013 238366 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.76 Å2 / Biso mean: 14.3826 Å2 / Biso min: 3.99 Å2
Refinement stepCycle: final / Resolution: 1.2→42.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 0 216 1041 7176
Biso mean--19.99 28.5 -
Num. residues----757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126339
X-RAY DIFFRACTIONf_angle_d1.4468618
X-RAY DIFFRACTIONf_chiral_restr0.086957
X-RAY DIFFRACTIONf_plane_restr0.0081110
X-RAY DIFFRACTIONf_dihedral_angle_d14.6632374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21360.20463940.18757495788999
1.2136-1.22790.19964080.174275637971100
1.2279-1.24280.16964320.156774007832100
1.2428-1.25860.16794080.143275317939100
1.2586-1.27510.16693940.13474727866100
1.2751-1.29260.15313920.124375747966100
1.2926-1.31110.14913930.117875637956100
1.3111-1.33070.15474060.116575257931100
1.3307-1.35140.14363910.11575417932100
1.3514-1.37360.14533950.108775377932100
1.3736-1.39730.14074010.105275347935100
1.3973-1.42270.13544350.104575237958100
1.4227-1.45010.1173960.095875837979100
1.4501-1.47970.11863760.082275407916100
1.4797-1.51180.10864180.078575507968100
1.5118-1.5470.10243900.073675227912100
1.547-1.58570.1093730.07375867959100
1.5857-1.62860.10233830.072876137996100
1.6286-1.67650.10444160.071775327948100
1.6765-1.73060.09893930.075775537946100
1.7306-1.79250.10813880.080875927980100
1.7925-1.86420.11493910.084575457936100
1.8642-1.94910.10664540.084675117965100
1.9491-2.05180.10364130.083675787991100
2.0518-2.18040.09833810.083875597940100
2.1804-2.34870.10863730.086675897962100
2.3487-2.58510.11273790.095376268005100
2.5851-2.9590.13533900.105576198009100
2.959-3.72780.12813930.107776248017100
3.7278-42.65830.14023990.12267431783097

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