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- PDB-4oso: The crystal structure of landomycin C-6 ketoreductase LanV with b... -

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Basic information

Entry
Database: PDB / ID: 4oso
TitleThe crystal structure of landomycin C-6 ketoreductase LanV with bound NADP and rabelomycin
ComponentsReductase homolog
KeywordsOxidoreductase/antibiotic / Rossmann fold / ketoreductase / NADPH binding / Oxidoreductase-antibiotic complex
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / nucleotide binding
Similarity search - Function
: / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
rabelomycin / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesStreptomyces cyanogenus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPaananen, P. / Niiranen, L. / Patrikainen, P. / Metsa-Ketela, M.
CitationJournal: Chem.Biol. / Year: 2014
Title: Structure-based engineering of angucyclinone 6-ketoreductases.
Authors: Patrikainen, P. / Niiranen, L. / Thapa, K. / Paananen, P. / Tahtinen, P. / Mantsala, P. / Niemi, J. / Metsa-Ketela, M.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Reductase homolog
B: Reductase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3788
Polymers55,0022
Non-polymers2,3766
Water1,74797
1
A: Reductase homolog
B: Reductase homolog
hetero molecules

A: Reductase homolog
B: Reductase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,75616
Polymers110,0044
Non-polymers4,75112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area21540 Å2
ΔGint-106 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.990, 91.990, 106.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Reductase homolog


Mass: 27501.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cyanogenus (bacteria) / Strain: S136 / Gene: lanV / Plasmid: pBAD derivative / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9ZGC1
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-2V4 / rabelomycin / (3R)-3,6,8-trihydroxy-3-methyl-3,4-dihydrotetraphene-1,7,12(2H)-trione


Mass: 338.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14O6
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris Propane, 0.2M sodium acetate, 18% PEG3350K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 16419 / Num. obs: 16276 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 11.52
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.560.9981.87193
2.56-2.630.8192.58199.4
2.63-2.710.7163.15199.4
2.71-2.790.613.65199.5
2.79-2.880.4974.53199.5
2.88-2.980.4015.76199.6
2.98-3.10.3396.69199.7
3.1-3.220.2798.07199.8
3.22-3.370.22210.5199.8
3.37-3.530.18112.63199.9
3.53-3.720.14315.09199.9
3.72-3.950.12816.54199.6
3.95-4.220.10219.96199.9
4.22-4.560.08522.62199.6
4.56-4.990.07924.27199.8
4.99-5.580.08422.46199.7
5.58-6.450.0822.871100
6.45-7.890.06225.95199.8
7.89-11.160.04731.17198.4
11.160.0428.93196.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
EDNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KWH

4kwh


Resolution: 2.5→69.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.06 / SU ML: 0.239 / SU R Cruickshank DPI: 5.1264 / Cross valid method: THROUGHOUT / ESU R: 5.126 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23466 800 4.9 %RANDOM
Rwork0.17447 ---
obs0.1776 15465 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.292 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å2-0 Å2
2---1.62 Å2-0 Å2
3---3.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→69.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 160 97 3847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023824
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3342.0195210
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0435496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50723.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0971528
X-RAY DIFFRACTIONr_chiral_restr0.1020.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212855
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4493.6271990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3885.4342484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0043.8591833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 58 -
Rwork0.27 1029 -
obs--92.99 %

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