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

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Basic information

Entry
Database: PDB / ID: 3csd
TitleActinorhodin Polyketide Ketoreductase Mutant P94L bound to NADPH and the Inhibitor Emodin
ComponentsPutative ketoacyl reductase
KeywordsOXIDOREDUCTASE / Antibiotic biosynthesis / NADP
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 / Resolution: 2.29 Å
AuthorsJavidpour, P.
CitationJournal: To be Published
Title: Actinorhodin Polyketide Ketoreductase Mutant P94L bound to NADPH and the Inhibitor Emodin
Authors: Javidpour, P.
History
DepositionApr 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,5338
Polymers58,9612
Non-polymers2,5726
Water3,279182
1
B: Putative ketoacyl reductase
A: Putative ketoacyl reductase
hetero molecules

B: Putative ketoacyl reductase
A: Putative 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 area21940 Å2
ΔGint-40.7 kcal/mol
Surface area32880 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-5.9 kcal/mol
Surface area19370 Å2
MethodPISA
3
B: Putative ketoacyl reductase
hetero molecules

A: Putative ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5338
Polymers58,9612
Non-polymers2,5726
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation4_643y+1,x-1,-z-21
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-2.6 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.089, 105.089, 123.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative ketoacyl reductase


Mass: 29480.404 Da / Num. of mol.: 2 / Mutation: P94L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: actIII / Plasmid: pET28c / 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.: 4 / Source method: obtained synthetically / Formula: C15H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
DetectorDate: Feb 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 35974 / % possible obs: 50 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.495 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.485 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20749 1795 5 %RANDOM
Rwork0.17253 ---
obs0.17431 34136 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 176 182 4110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8882.0245448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88523150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06315612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9151537
X-RAY DIFFRACTIONr_chiral_restr0.1790.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21852
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22709
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3151.52583
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18224000
X-RAY DIFFRACTIONr_scbond_it3.30731673
X-RAY DIFFRACTIONr_scangle_it5.1434.51448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 117 -
Rwork0.197 2457 -
obs--100 %

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