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- PDB-2rh4: Actinorhodin ketoreductase, actKR, with NADPH and Inhibitor Emodin -

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Basic information

Entry
Database: PDB / ID: 2rh4
TitleActinorhodin ketoreductase, actKR, with NADPH and Inhibitor Emodin
ComponentsActinorhodin Polyketide Ketoreductase
KeywordsOXIDOREDUCTASE / polyketide / actinorhodin / ketoreductase / combinatorial biosynthesis / short chain dehydrogenase/reductase
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
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / Chem-NDP / Putative ketoacyl reductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKorman, T.P. / Tsai, S.-C.
CitationJournal: Biochemistry / Year: 2008
Title: Inhibition kinetics and emodin cocrystal structure of a type II polyketide ketoreductase
Authors: Korman, T.P. / Tan, Y.H. / Wong, J. / Luo, R. / Tsai, S.-C.
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Aug 30, 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: Actinorhodin Polyketide Ketoreductase
B: Actinorhodin Polyketide Ketoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9655
Polymers58,2042
Non-polymers1,7613
Water4,828268
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)119,93010
Polymers116,4084
Non-polymers3,5226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area17990 Å2
ΔGint-74 kcal/mol
Surface area35180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.000, 104.000, 123.400
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 Actinorhodin Polyketide Ketoreductase / E.C.1.3.1.- / ketoacyl reductase


Mass: 29101.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: actIII / Plasmid: pYT284 / Production host: Escherichia coli (E. coli) / 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3.8-4.8 M sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2005
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Si(111) Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs
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. all: 34802 / Num. obs: 33667 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 33
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1x7h

1x7h


Resolution: 2.3→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3355 -RANDOM
Rwork0.179 ---
all-34802 --
obs-33667 96.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 116 268 4234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_angle_deg1.287
X-RAY DIFFRACTIONc_mcbond_it1.2711.5
X-RAY DIFFRACTIONc_mcangle_it2.0442
X-RAY DIFFRACTIONc_scbond_it2.2052
X-RAY DIFFRACTIONc_scangle_it3.1462.5
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection
Rfree0.204 326
Rwork0.179 -
obs-3404

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