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- PDB-3e1h: Crystal structure of a type III polyketide synthase PKSIIINc from... -

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Basic information

Entry
Database: PDB / ID: 3e1h
TitleCrystal structure of a type III polyketide synthase PKSIIINc from Neurospora crassa
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / Resorcinolic lipid synthase / Type III PKS / Acyltransferase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
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 speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsGoyal, A. / Rahman, A. / Sankaranarayanan, R.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Structural insights into biosynthesis of resorcinolic lipids by a type III polyketide synthase in Neurospora crassa
Authors: Goyal, A. / Saxena, P. / Rahman, A. / Singh, P.K. / Kasbekar, D.P. / Gokhale, R.S. / Sankaranarayanan, R.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)99,1862
Polymers99,1862
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-14 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.023, 104.960, 105.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / PKSIIINc


Mass: 49592.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Strain: 74-OR23-1A (FGSC 987) / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7S6N4, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, Isopropanol, Sodium acetate, HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 2007 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→25 Å / Num. all: 24396 / Num. obs: 24396 / % possible obs: 97.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.24 / Num. unique all: 2150 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGZ and 1TED

1cgz

1ted


Resolution: 2.58→25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.896 / SU B: 11.38 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26016 1229 5.1 %RANDOM
Rwork0.21346 ---
obs0.21593 23093 97.99 %-
all-23093 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---1.45 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.58→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 0 0 413 6181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225892
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9868006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49923.86228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09815982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7821538
X-RAY DIFFRACTIONr_chiral_restr0.0860.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024442
X-RAY DIFFRACTIONr_nbd_refined0.2310.23226
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.24
X-RAY DIFFRACTIONr_mcbond_it0.5221.53889
X-RAY DIFFRACTIONr_mcangle_it0.93726140
X-RAY DIFFRACTIONr_scbond_it1.17232210
X-RAY DIFFRACTIONr_scangle_it1.9314.51866
LS refinement shellResolution: 2.591→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 85 -
Rwork0.33 1527 -
obs--90.92 %

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