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- PDB-4yxf: MupS, a 3-oxoacyl (ACP) reductase involved in Mupirocin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 4yxf
TitleMupS, a 3-oxoacyl (ACP) reductase involved in Mupirocin biosynthesis
ComponentsMupS
KeywordsOXIDOREDUCTASE / 3-oxoacyl (ACP) reductase / mupirocin
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsTill, M. / Race, P.R.
CitationJournal: To Be Published
Title: MupS, a 3-oxoacyl (ACP) reductase involved in Mupirocin biosynthesis
Authors: Till, M. / Race, P.R.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MupS
B: MupS


Theoretical massNumber of molelcules
Total (without water)54,6882
Polymers54,6882
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-24 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.080, 94.080, 194.341
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein MupS


Mass: 27343.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: mupS / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RL53
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 4.54 Å3/Da / Density % sol: 72.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Molecular dimensions morpheus screen well C6 - NPS ligands, EDO_P8K precipitant mix
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→81.475 Å / Num. all: 28109 / Num. obs: 28109 / % possible obs: 100 % / Redundancy: 8.8 % / Rpim(I) all: 0.065 / Rrim(I) all: 0.191 / Rsym value: 0.18 / Net I/av σ(I): 3.669 / Net I/σ(I): 10.6 / Num. measured all: 248741
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.8591.120.63642540290.3931.123100
2.85-3.029.50.69213628238080.2370.6924.5100
3.02-3.239.60.391.83474536070.1330.396.6100
3.23-3.498.90.22432987933630.080.2249.2100
3.49-3.8290.1534.42800931000.0540.15312.6100
3.82-4.279.50.11462696228460.040.11416.3100
4.27-4.938.40.0897.32102425150.0340.08918.6100
4.93-6.048.10.0956.81741121460.0370.09516.4100
6.04-8.547.50.0827.61280317050.0340.08216.699.9
8.54-47.045.30.0559.752019900.0270.05518.999

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.04 Å
Translation2.5 Å47.04 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSU

3osu


Resolution: 2.7→47.08 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2285 / WRfactor Rwork: 0.1825 / FOM work R set: 0.8535 / SU B: 7.735 / SU ML: 0.16 / SU R Cruickshank DPI: 0.331 / SU Rfree: 0.2603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1410 5 %RANDOM
Rwork0.2037 ---
obs0.2059 26656 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.54 Å2 / Biso mean: 42.012 Å2 / Biso min: 18.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å21.75 Å20 Å2
2--1.75 Å20 Å2
3----5.69 Å2
Refinement stepCycle: final / Resolution: 2.7→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 0 21 3320
Biso mean---43.67 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193332
X-RAY DIFFRACTIONr_angle_refined_deg2.4651.9664518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8055449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81923.871124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.61915526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1161521
X-RAY DIFFRACTIONr_chiral_restr0.1630.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022461
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 86 -
Rwork0.339 1941 -
all-2027 -
obs--100 %

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