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- PDB-1x7g: Actinorhodin Polyketide Ketoreductase, act KR, with NADP bound -

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Basic information

Entry
Database: PDB / ID: 1x7g
TitleActinorhodin Polyketide Ketoreductase, act KR, with NADP bound
ComponentsPutative ketoacyl reductase
KeywordsOXIDOREDUCTASE / polyketide / ketoreductase / short chain dehydrogenase/reductase / combinatorial biosynthesis / actinorhodin / antibiotic
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / monocarboxylic acid metabolic process / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative ketoacyl reductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKorman, T.P. / Hill, J.A. / Vu, T.N.
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
DepositionAug 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Putative ketoacyl reductase
B: Putative ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0734
Polymers54,5862
Non-polymers1,4872
Water4,900272
1
A: Putative ketoacyl reductase
B: Putative ketoacyl reductase
hetero molecules

A: Putative ketoacyl reductase
B: Putative ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1468
Polymers109,1724
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area16630 Å2
ΔGint-80 kcal/mol
Surface area35060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.610, 104.610, 124.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe second part of the biological assembly is generated by the two fold axis: X-Y, -Y, 1/3-Z

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Components

#1: Protein Putative ketoacyl reductase / act KR / 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) / Strain: CH999 / Gene: actIII / Plasmid: pET28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
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


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 4.76 Å3/Da / Density % sol: 74.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 35529 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26.6 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.115 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.857 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.42 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 159974.9 / 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
Rfree0.245 1722 5.1 %RANDOM
Rwork0.211 ---
obs0.211 33832 95.4 %-
all-35554 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6513 Å2 / ksol: 0.365452 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å24.17 Å20 Å2
2--2.94 Å20 Å2
3----5.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 96 272 4047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 267 5.1 %
Rwork0.251 4976 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5NADP.PARNADP.TOP

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