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- PDB-3euq: X-ray structural of a type III pentaketide synthase from Neurospo... -

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Basic information

Entry
Database: PDB / ID: 3euq
TitleX-ray structural of a type III pentaketide synthase from Neurospora crassa
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / alpha helix / 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 / SYNCHROTRON / SAD / Resolution: 2.1 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: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)163,4036
Polymers162,8384
Non-polymers5652
Water14,844824
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7013
Polymers81,4192
Non-polymers2821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-18 kcal/mol
Surface area25250 Å2
MethodPISA
2
C: Putative uncharacterized protein
hetero molecules

D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)81,7013
Polymers81,4192
Non-polymers2821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area5470 Å2
ΔGint-19 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.689, 105.116, 105.078
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative uncharacterized protein


Mass: 40709.539 Da / Num. of mol.: 4 / Fragment: UNP residues 10-388 / Mutation: F252G
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-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.36 Å3/Da / Density % sol: 47.84 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 80720

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.195 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25586 4262 5 %RANDOM
Rwork0.19847 ---
obs0.20137 80720 96.28 %-
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: 27.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20.94 Å2
2---0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11400 0 38 824 12262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211676
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9915854
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97751512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47723.784444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.138151932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8811576
X-RAY DIFFRACTIONr_chiral_restr0.0850.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028744
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.25893
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.28043
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.2175
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5261.57761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.852212144
X-RAY DIFFRACTIONr_scbond_it1.48834397
X-RAY DIFFRACTIONr_scangle_it2.3574.53710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 268 -
Rwork0.223 5505 -
obs--89.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0416-0.38910.28790.74230.01550.78320.05110.1063-0.0622-0.065-0.0370.03290.12860.0211-0.0142-0.0783-0.00140.0015-0.092-0.0063-0.0822.6787-4.570425.5056
20.665-0.19890.19630.9136-0.02571.1017-0.0218-0.04160.08390.0957-0.0148-0.0897-0.0010.08850.0366-0.1104-0.01310.0026-0.10070.0101-0.065435.193116.703845.1704
31.409-0.3345-0.49310.7090.01810.68470.09290.16380.1095-0.0526-0.0411-0.0236-0.1106-0.0485-0.0519-0.1164-0.005-0.0005-0.08470.0099-0.073612.47314.419778.2259
40.60550.0645-0.21650.72960.03570.947-0.02730.0415-0.0903-0.10820.0092-0.02510.1180.0610.0181-0.09570.0328-0.0077-0.09540.0124-0.0533-0.217635.68847.4898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 388
2X-RAY DIFFRACTION2B14 - 388
3X-RAY DIFFRACTION3C14 - 388
4X-RAY DIFFRACTION4D14 - 388

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