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- PDB-3ri3: Actinorhodin Polyketide Ketoreductase Mutant P94L bound to NADPH ... -

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Basic information

Entry
Database: PDB / ID: 3ri3
TitleActinorhodin Polyketide Ketoreductase Mutant P94L bound to NADPH and the Inhibitor Emodin
Componentsketoacyl reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / actinorhodin / polyketide / ketoreductase / short-chain dehydrogenase/reductase / Rossmann fold / Type II polyketide ketoreductase / OXIDOREDUCTASE-OXIDOREDUCTASE 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
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / Chem-NDP / Putative ketoacyl reductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.292 Å
AuthorsJavidpour, P. / Tsai, S.-C.
CitationJournal: Biochemistry / Year: 2011
Title: Structural and Biochemical Analyses of Regio- and Stereospecificities Observed in a Type II Polyketide Ketoreductase.
Authors: Javidpour, P. / Korman, T.P. / Shakya, G. / Tsai, S.C.
History
DepositionApr 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version
Revision 1.4Sep 13, 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
B: ketoacyl reductase
A: ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5338
Polymers58,9612
Non-polymers2,5726
Water1,928107
1
B: ketoacyl reductase
A: ketoacyl reductase
hetero molecules

B: ketoacyl reductase
A: ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,06516
Polymers117,9224
Non-polymers5,14412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_643y+1,x-1,-z-21
Buried area21870 Å2
ΔGint-54 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.089, 105.089, 123.650
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 ketoacyl reductase


Mass: 29480.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: actIII, SCBAC28G1.12c, SCO5086 / Plasmid: pET28 / 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.: 4 / Source method: obtained synthetically / Formula: C15H10O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 35974 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.11 / Χ2: 1.223 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.29-2.3310.90.49517571.0151100
2.33-2.37110.43217711.041100
2.37-2.4211.10.38917801.0531100
2.42-2.4711.10.37117461.0691100
2.47-2.5211.10.32317891.0811100
2.52-2.5811.10.28717891.0751100
2.58-2.6411.10.25717781.0471100
2.64-2.72110.24817861.0941100
2.72-2.7911.10.19417761.091100
2.79-2.8911.10.16617751.0911100
2.89-2.9911.10.14317901.125199.9
2.99-3.11110.12817841.2561100
3.11-3.25110.10917991.2291100
3.25-3.42110.117941.31100
3.42-3.6310.90.0918081.291100
3.63-3.9210.70.08618061.3461100
3.92-4.3110.60.07418131.3251100
4.31-4.9310.20.07918231.6061100
4.93-6.2110.90.08318681.4251100
6.21-5010.20.11419421.9291100

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.783 / Packing: 0.398
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral99.6 0

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RHR

2rhr


Resolution: 2.292→45.505 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 1794 4.99 %
Rwork0.182 --
obs0.1834 35919 99.94 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.154 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 115.29 Å2 / Biso mean: 45.8395 Å2 / Biso min: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.6214 Å20 Å2-0 Å2
2--3.6214 Å20 Å2
3----7.2428 Å2
Refinement stepCycle: LAST / Resolution: 2.292→45.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 176 107 4035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083991
X-RAY DIFFRACTIONf_angle_d1.415448
X-RAY DIFFRACTIONf_chiral_restr0.14633
X-RAY DIFFRACTIONf_plane_restr0.004686
X-RAY DIFFRACTIONf_dihedral_angle_d16.1321406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2917-2.35360.27071240.210725662690
2.3536-2.42290.20391320.190926102742
2.4229-2.50110.25161430.191525852728
2.5011-2.59040.23651300.194325822712
2.5904-2.69410.21951310.199226342765
2.6941-2.81670.26681400.204625622702
2.8167-2.96520.20941360.2126102746
2.9652-3.1510.2251370.190426242761
3.151-3.39420.20431450.177926272772
3.3942-3.73560.18661280.156626492777
3.7356-4.27580.18051470.165826312778
4.2758-5.38570.19151520.167226682820
5.3857-45.51380.21761490.195127772926

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