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- PDB-5l4l: polyketide ketoreductase SimC7 - ternary complex with NADP+ and 7... -

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Basic information

Entry
Database: PDB / ID: 5l4l
Titlepolyketide ketoreductase SimC7 - ternary complex with NADP+ and 7-oxo-SD8
ComponentsSimC7
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductase / Ketoreductase / Simocyclinone / DNA gyrase inhibitor
Function / homology
Function and homology information


NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-oxo-simocyclinone D8 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative hydroxylase/dehydratase
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSchafer, M. / Stevenson, C.E.M. / Wilkinson, B. / Lawson, D.M. / Buttner, M.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I002197/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilDoctoral Training Partnership United Kingdom
CitationJournal: Cell Chem Biol / Year: 2016
Title: Substrate-Assisted Catalysis in Polyketide Reduction Proceeds via a Phenolate Intermediate.
Authors: Schafer, M. / Stevenson, C.E. / Wilkinson, B. / Lawson, D.M. / Buttner, M.J.
History
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / struct_site_gen
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_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _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.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SimC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0434
Polymers32,2781
Non-polymers1,7663
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-4 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.930, 53.660, 102.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SimC7


Mass: 32277.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A twenty residue nickel affinity tag with sequence MGSSHHHHHHSSGLVPRGSH was appended to the N-terminus of the native amino acid sequence being derived from the pET-15b vector construct named pET15b-NB-C7
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: simC7 / Plasmid: pET15b-NB-C7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: G9VYV4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-7OX / 7-oxo-simocyclinone D8


Mass: 930.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H40ClNO18
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→47.52 Å / Num. obs: 90009 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Net I/σ(I): 17.5 / Num. measured all: 1159483
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.2-1.2312.31.208199.9
5.37-47.5211.60.043199.9

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3Z

5l3z


Resolution: 1.2→47.52 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.066 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.032
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1489 4476 5 %RANDOM
Rwork0.1257 ---
obs0.1269 85532 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.37 Å2 / Biso mean: 17.848 Å2 / Biso min: 8.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.2→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 101 336 2482
Biso mean--16.88 31.94 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192427
X-RAY DIFFRACTIONr_bond_other_d0.0020.022283
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9663370
X-RAY DIFFRACTIONr_angle_other_deg0.93635241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.96922.12199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52315351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.651529
X-RAY DIFFRACTIONr_chiral_restr0.0920.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213018
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02543
X-RAY DIFFRACTIONr_mcbond_it1.61.5091224
X-RAY DIFFRACTIONr_mcbond_other1.5961.5071223
X-RAY DIFFRACTIONr_mcangle_it1.9392.281561
X-RAY DIFFRACTIONr_rigid_bond_restr2.04234709
X-RAY DIFFRACTIONr_sphericity_free24.753584
X-RAY DIFFRACTIONr_sphericity_bonded7.92954887
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 321 -
Rwork0.218 6265 -
all-6265 -
obs--99.86 %

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