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- PDB-5l45: polyketide ketoreductase SimC7 - apo crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 5l45
Titlepolyketide ketoreductase SimC7 - apo crystal form 2
ComponentsSimC7
KeywordsHYDROLASE / short-chain dehydrogenase/reductase / Ketoreductase / Simocyclinone / DNA gyrase inhibitor
Function / homologyNAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative hydroxylase/dehydratase
Function and homology information
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 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

Downloads & links

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Assembly

Deposited unit
A: SimC7
B: SimC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8414
Polymers64,5552
Non-polymers2862
Water3,639202
1
A: SimC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4722
Polymers32,2781
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SimC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3702
Polymers32,2781
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.950, 64.840, 91.480
Angle α, β, γ (deg.)90.000, 105.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SimC7


Mass: 32277.582 Da / Num. of mol.: 2
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop

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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: 1.9→54.88 Å / Num. obs: 47271 / % possible obs: 99.1 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.035 / Rrim(I) all: 0.094 / Net I/σ(I): 13.6 / Num. measured all: 336053 / Scaling rejects: 1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.956.71.99197.5
8.5-54.886.50.027199.5

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3Z

5l3z


Resolution: 1.9→54.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.967 / SU ML: 0.135 / SU R Cruickshank DPI: 0.1495 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.138
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 2357 5 %RANDOM
Rwork0.1946 ---
obs0.1963 44913 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 101.97 Å2 / Biso mean: 49.185 Å2 / Biso min: 20.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å22.86 Å2
2---1.74 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.9→54.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 13 210 4298
Biso mean--58.39 49.54 -
Num. residues----559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194211
X-RAY DIFFRACTIONr_bond_other_d0.0020.024081
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9715758
X-RAY DIFFRACTIONr_angle_other_deg0.90739339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64822.099162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67615614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.161545
X-RAY DIFFRACTIONr_chiral_restr0.070.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
X-RAY DIFFRACTIONr_mcbond_it1.1853.1722249
X-RAY DIFFRACTIONr_mcbond_other1.1853.1712248
X-RAY DIFFRACTIONr_mcangle_it1.8644.752812
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 192 -
Rwork0.342 3237 -
all-3429 -
obs--97.47 %
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)
12.5254-0.710.16274.5934-3.26084.32440.09420.23470.0214-0.2114-0.1459-0.32670.08840.28150.05170.04730.04940.02730.23520.03920.112-14.494219.05863.9759
24.8903-1.8080.42191.4124-0.30370.5952-0.1174-0.11650.59080.14960.0776-0.0063-0.3775-0.10120.03980.24880.05720.00170.050.02330.2043-20.51224.557718.2468
31.4385-0.05630.89531.1620.21142.29330.0901-0.0992-0.08810.07710.0081-0.22260.00220.1437-0.09820.055-0.00030.04570.03670.02930.16-6.062117.166728.529
44.9251-0.2860.27654.04740.43964.70750.1387-0.54120.01890.4391-0.07290.42770.105-0.3388-0.06570.36130.01350.07080.21440.02230.2279-3.685150.404236.2244
52.9016-1.80440.34674.3449-0.38640.93880.08210.1437-0.2267-0.1534-0.06060.76580.0736-0.2269-0.02150.0735-0.06060.00520.12820.00520.251-4.774747.084420.8179
61.8515-0.3586-0.44023.19550.25851.2340.01240.0696-0.07730.05550.0485-0.0860.0349-0.0633-0.06090.005-0.0141-0.00310.10160.01010.030710.352539.097818.2688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 73
2X-RAY DIFFRACTION2A74 - 143
3X-RAY DIFFRACTION3A144 - 279
4X-RAY DIFFRACTION4B-1 - 56
5X-RAY DIFFRACTION5B57 - 150
6X-RAY DIFFRACTION6B151 - 279

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