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- PDB-1xr3: Actinorhodin Polyketide Ketoreductase with NADP and the Inhibitor... -

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Basic information

Entry
Database: PDB / ID: 1xr3
TitleActinorhodin Polyketide Ketoreductase with NADP and the Inhibitor Isoniazid bound
ComponentsACTINORHODIN POLYKETIDE KETOREDUCTASE
KeywordsOXIDOREDUCTASE / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / steroid metabolic process / antibiotic biosynthetic process / oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
4-(DIAZENYLCARBONYL)PYRIDINE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative ketoacyl reductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsKorman, T.P. / Hill, J.A. / Vu, T.N. / Tsai, S.C.
CitationJournal: Biochemistry / Year: 2004
Title: Structural analysis of actinorhodin polyketide ketoreductase: cofactor binding and substrate specificity.
Authors: Korman, T.P. / Hill, J.A. / Vu, T.N. / Tsai, S.C.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ACTINORHODIN POLYKETIDE KETOREDUCTASE
B: ACTINORHODIN POLYKETIDE KETOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3436
Polymers54,5862
Non-polymers1,7574
Water0
1
A: ACTINORHODIN POLYKETIDE KETOREDUCTASE
B: ACTINORHODIN POLYKETIDE KETOREDUCTASE
hetero molecules

A: ACTINORHODIN POLYKETIDE KETOREDUCTASE
B: ACTINORHODIN POLYKETIDE KETOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,68612
Polymers109,1724
Non-polymers3,5148
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area18210 Å2
ΔGint-64 kcal/mol
Surface area34370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.224, 104.224, 124.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -X, Y-X, 2/3-Z

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Components

#1: Protein ACTINORHODIN POLYKETIDE KETOREDUCTASE


Mass: 27293.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: actIII / Plasmid: pET28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P16544, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ISZ / 4-(DIAZENYLCARBONYL)PYRIDINE / ISONIAZID / TUBAZID / RIMITSID / ISONICOTINYLHYDRAZINE / LANIZID / NYDRAZID / Isoniazid


Mass: 135.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5N3O / Comment: antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 75 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 11, 2004 / Details: mirrors
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 21721 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Biso Wilson estimate: 37.7 Å2 / Net I/σ(I): 16.1
Reflection shellResolution: 2.71→2.76 Å / Redundancy: 7.2 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X7G

1x7g


Resolution: 2.71→48.06 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 74691.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2025 9.9 %RANDOM
Rwork0.212 ---
all0.212 21685 --
obs0.212 20523 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.4248 Å2 / ksol: 0.359503 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å28.34 Å20 Å2
2--3.9 Å20 Å2
3----7.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.71→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 116 0 3838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.71→2.88 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 319 10.5 %
Rwork0.328 2721 -
obs-1068 85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DRGCNS.PARDRGCNS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5NADP.PARNADP.TOP

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