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- PDB-3eut: X-ray crystal structure of a type III pentaketide synthase from N... -

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Basic information

Entry
Database: PDB / ID: 3eut
TitleX-ray crystal structure of a type III pentaketide synthase from Neurospora crassa
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / ORAS / 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
icosanoic acid / Chalcone synthase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, H. / Brunzelle, J.S. / Nair, S.K.
CitationJournal: Chem.Biol. / Year: 2008
Title: Distinct Structural Elements Dictate the Specificity of the Type III Pentaketide Synthase from Neurospora crassa.
Authors: Rubin-Pitel, S.B. / Zhang, H. / Vu, T. / Brunzelle, J.S. / Zhao, H. / Nair, S.K.
History
DepositionOct 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,8246
Polymers163,1994
Non-polymers6252
Water14,502805
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9123
Polymers81,5992
Non-polymers3131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-11 kcal/mol
Surface area25610 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9123
Polymers81,5992
Non-polymers3131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-11 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.867, 105.925, 104.124
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative uncharacterized protein


Mass: 40799.660 Da / Num. of mol.: 4 / Fragment: UNP residues 10-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: NCU04801, NCU04801.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7S6N4
#2: Chemical ChemComp-DCR / icosanoic acid


Mass: 312.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H40O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.14 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 92963

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.831 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22476 4891 5 %RANDOM
Rwork0.17361 ---
obs0.17616 92963 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.981 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å2-0.2 Å2
2---2.8 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11428 0 44 805 12277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211714
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9915906
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76251512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96123.75448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191576
X-RAY DIFFRACTIONr_chiral_restr0.0870.21808
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028780
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.25500
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.28097
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2844
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6561.57770
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.097212156
X-RAY DIFFRACTIONr_scbond_it1.97534429
X-RAY DIFFRACTIONr_scangle_it3.0614.53750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 298 -
Rwork0.2 6116 -
obs--86.92 %

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