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

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Basic information

Entry
Database: PDB / ID: 3qrw
TitleActinorhodin Polyketide Ketoreductase Mutant P94L bound to NADPH
Componentsketoacyl reductase
KeywordsOXIDOREDUCTASE / actinorhodin / polyketide / ketoreductase / short-chain dehydrogenase/reductase / Type II polyketide ketoreductase / Rossmann fold
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
FORMIC ACID / Chem-NDP / Putative ketoacyl reductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.792 Å
AuthorsKorman, T.P. / Javidpour, 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
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 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.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,4985
Polymers58,9612
Non-polymers1,5373
Water73941
1
A: ketoacyl reductase
B: ketoacyl reductase
hetero molecules

A: ketoacyl reductase
B: ketoacyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,99510
Polymers117,9224
Non-polymers3,0746
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area17490 Å2
ΔGint-88 kcal/mol
Surface area34610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.583, 104.583, 123.588
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 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) / 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-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 62.83 %
Crystal growTemperature: 298 K / Method: hanging-drop vapor diffusion / pH: 7.5
Details: 3.8-4.8 M sodium formate, pH 7.5, hanging-drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19775 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.8511.10.4641100
2.85-2.911.10.4071100
2.9-2.9611.10.3751100
2.96-3.0211.10.31100
3.02-3.0811.10.2551100
3.08-3.15110.2231100
3.15-3.2311.10.1911100
3.23-3.32110.1741100
3.32-3.4211.10.151100
3.42-3.5310.90.1251100
3.53-3.6510.90.1041100
3.65-3.810.90.091100
3.8-3.9710.80.0881100
3.97-4.1810.70.0661100
4.18-4.4410.60.055199.9
4.44-4.79100.0481100
4.79-5.2711.10.0451100
5.27-6.03110.0531100
6.03-7.5910.80.0451100
7.59-50100.031199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.6 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.79 Å37.5 Å
Translation2.79 Å37.5 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.792→37.499 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / SU R Cruickshank DPI: 0.536 / σ(F): 0 / Phase error: 20.82 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2255 1002 5.11 %
Rwork0.1609 --
obs0.1641 19609 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.944 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7152 Å2-0 Å2-0 Å2
2--3.7152 Å2-0 Å2
3----7.4305 Å2
Refinement stepCycle: LAST / Resolution: 2.792→37.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 99 41 3939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083955
X-RAY DIFFRACTIONf_angle_d1.1975386
X-RAY DIFFRACTIONf_dihedral_angle_d19.0951413
X-RAY DIFFRACTIONf_chiral_restr0.072639
X-RAY DIFFRACTIONf_plane_restr0.005691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7919-2.9390.29481370.22582521X-RAY DIFFRACTION95
2.939-3.12310.27141560.20182580X-RAY DIFFRACTION98
3.1231-3.36410.27631550.1862627X-RAY DIFFRACTION99
3.3641-3.70230.20271300.15862641X-RAY DIFFRACTION99
3.7023-4.23740.21561480.14272664X-RAY DIFFRACTION100
4.2374-5.33630.17851520.12952722X-RAY DIFFRACTION100
5.3363-37.50260.22141240.15722852X-RAY DIFFRACTION100

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