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- PDB-2rhr: P94L actinorhodin ketordeuctase mutant, with NADPH and Inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 2rhr
TitleP94L actinorhodin ketordeuctase mutant, 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 / 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 / Resolution: 2.5 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 9, 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Actinorhodin Polyketide Ketoreductase
A: Actinorhodin Polyketide Ketoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2676
Polymers58,2362
Non-polymers2,0314
Water3,045169
1
B: Actinorhodin Polyketide Ketoreductase
A: Actinorhodin Polyketide Ketoreductase
hetero molecules

B: Actinorhodin Polyketide Ketoreductase
A: Actinorhodin Polyketide Ketoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,53512
Polymers116,4724
Non-polymers4,0638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area18110 Å2
ΔGint-74 kcal/mol
Surface area35460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.778, 104.778, 123.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Actinorhodin Polyketide Ketoreductase / E.C.1.3.1.- / ketoacyl reductase


Mass: 29118.004 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 / 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 / Emodin


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 3.8-4.8 M sodium formate, pH 7.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2006
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 27840 / Num. obs: 27802 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2725 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementStarting model: PDB ID 1X7H
Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2643 9.6 %RANDOM
Rwork0.184 ---
all-27602 --
obs-26626 96.5 %-
Solvent computationBsol: 57.584 Å2
Displacement parametersBiso mean: 54.769 Å2
Baniso -1Baniso -2Baniso -3
1-5.095 Å20 Å20 Å2
2--5.095 Å20 Å2
3----10.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 136 169 4046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.336
X-RAY DIFFRACTIONc_mcbond_it1.3981.5
X-RAY DIFFRACTIONc_scbond_it2.3392
X-RAY DIFFRACTIONc_mcangle_it2.3772
X-RAY DIFFRACTIONc_scangle_it3.5382.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4nadp.parnadp.top
X-RAY DIFFRACTION5emo.paremo.top

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