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- PDB-4kwi: The crystal structure of angucycline C-6 ketoreductase LanV with ... -

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Basic information

Entry
Database: PDB / ID: 4kwi
TitleThe crystal structure of angucycline C-6 ketoreductase LanV with bound NADP and 11-deoxy-6-oxylandomycinone
ComponentsReductase homolog
KeywordsOxidoreductase/antibiotic / Rossmann fold / ketoreductase / NADPH binding / Oxidoreductase-antibiotic complex
Function / homology
Function and homology information


oxidoreductase 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
Chem-1TJ / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Reductase homolog
Similarity search - Component
Biological speciesStreptomyces cyanogenus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPaananen, P. / Patrikainen, P. / Mantsala, P. / Niemi, J. / Niiranen, L. / Metsa-Ketela, M.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and functional analysis of angucycline C-6 ketoreductase LanV involved in landomycin biosynthesis.
Authors: Paananen, P. / Patrikainen, P. / Kallio, P. / Mantsala, P. / Niemi, J. / Niiranen, L. / Metsa-Ketela, M.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,2367
Polymers55,0022
Non-polymers2,2345
Water4,306239
1
A: Reductase homolog
B: Reductase homolog
hetero molecules

A: Reductase homolog
B: Reductase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,47114
Polymers110,0044
Non-polymers4,46710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area18250 Å2
ΔGint-89 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.610, 92.610, 106.330
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 Reductase homolog


Mass: 27501.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cyanogenus (bacteria) / Gene: lanV / Plasmid: pBAD / 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-1TJ / 1,8-dihydroxy-3-methyltetraphene-6,7,12(5H)-trione / 11-DEOXY-6-OXYLANDOMYCINONE


Mass: 320.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H12O5
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris-Propane, 0.2M sodium acetate, 18% PEG3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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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: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31692 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 31.971 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 12.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2-2.056.90.9292.12146922137213790.9
2.05-2.110.7352.94166782259100
2.11-2.170.6593.35162032199100
2.17-2.230.5334.28156832124100
2.23-2.310.474.9153942093100
2.31-2.390.3925.89147091999100
2.39-2.480.3626.3114460196599.9
2.48-2.580.3127.35136211857100
2.58-2.690.2558.813227180199.9
2.69-2.830.20910.1612694173599.8
2.83-2.980.16712.3611957164099.7
2.98-3.160.13814.4311284155499.7
3.16-3.380.10218.5810677148699.7
3.38-3.650.07523.389697136299.7
3.65-40.06426.489047127899.3
4-4.470.0531.168066116399.4
4.47-5.160.04433.227207103799.4
5.16-6.320.04431.18614088199
6.32-8.940.03233.73477770598.3
8.940.02437.29254341796.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
EDNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KWH

4kwh


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2004 / WRfactor Rwork: 0.1583 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.857 / SU B: 9.088 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2037 / SU Rfree: 0.1695 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1598 5 %RANDOM
Rwork0.1823 ---
obs0.1845 31680 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 27.0109 Å2 / Biso min: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-0 Å2
2---0.86 Å2-0 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 0 151 239 4087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023933
X-RAY DIFFRACTIONr_angle_refined_deg1.3662.0135358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0485511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51923.691149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4715598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4911529
X-RAY DIFFRACTIONr_chiral_restr0.1060.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212957
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 94 -
Rwork0.281 1844 -
all-1938 -
obs-1938 90.06 %
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)
10.81540.2243-0.340.3655-0.10110.3959-0.01330.06350.096-0.02370.05420.13210.0553-0.0117-0.04090.0312-0.0091-0.00950.02940.02340.0486-23.13030.0403-27.7398
20.52270.2311-0.05350.8977-0.18930.2325-0.0272-0.0518-0.1392-0.02040.0137-0.04150.00020.01160.01350.03150.01550.00740.03660.0140.0377-1.1813-21.8845-22.4385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 253
2X-RAY DIFFRACTION2B-2 - 253

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