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- PDB-5l40: polyketide ketoreductase SimC7 - apo crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5l40
Titlepolyketide ketoreductase SimC7 - apo crystal form 1
Componentspolyketide ketoreductase SimC7
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
Putative hydroxylase/dehydratase
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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

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Assembly

Deposited unit
A: polyketide ketoreductase SimC7


Theoretical massNumber of molelcules
Total (without water)32,2781
Polymers32,2781
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.380, 52.380, 213.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein polyketide ketoreductase SimC7 / polyketide ketoreductase


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
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: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.6→53.4 Å / Num. obs: 40514 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Rrim(I) all: 0.069 / Net I/σ(I): 20 / Num. measured all: 435288
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.6410.91.814199.7
7.16-53.48.70.025199.9

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3Z

5l3z


Resolution: 1.6→53.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.002 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0861 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2010 5 %RANDOM
Rwork0.1892 ---
obs0.1907 38504 99.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.87 Å2 / Biso mean: 34.56 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 1.6→53.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 0 176 2243
Biso mean---37.21 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192162
X-RAY DIFFRACTIONr_bond_other_d0.0020.022092
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9712961
X-RAY DIFFRACTIONr_angle_other_deg0.9534789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89922.02289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04215322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7081526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_mcbond_it1.1691.6551146
X-RAY DIFFRACTIONr_mcbond_other1.1671.6551145
X-RAY DIFFRACTIONr_mcangle_it1.6912.481440
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 128 -
Rwork0.297 2807 -
all-2935 -
obs--99.63 %
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)
17.2156-1.53270.2466.41310.08826.47550.21870.51590.008-0.3806-0.32420.3024-0.1118-0.37940.10550.07260.0842-0.0540.1229-0.05530.044935.9347-0.80714.6453
23.4379-0.68280.62652.48271.04234.76530.32540.53550.2536-0.5343-0.2176-0.1441-0.5940.1143-0.10780.2140.07480.05360.09290.0350.071341.23358.88186.4307
32.1389-1.8382-0.39893.43710.32082.4880.1066-0.06070.19440.0122-0.0994-0.42530.00980.4265-0.00720.0145-0.0074-0.00380.08540.01980.05450.9404-3.740919.7743
43.1501-0.4105-0.8852.76750.69682.82360.0452-0.05420.10890.11080.0868-0.2889-0.08160.5285-0.1320.0484-0.02-0.01740.1041-0.01770.034354.1063-7.34520.6482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 38
2X-RAY DIFFRACTION2A39 - 100
3X-RAY DIFFRACTION3A101 - 218
4X-RAY DIFFRACTION4A219 - 280

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