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- PDB-5zi0: Ketoreductase LbCR mutant - M8 -

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Basic information

Entry
Database: PDB / ID: 5zi0
TitleKetoreductase LbCR mutant - M8
Components3-oxoacyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / ketoreductase / short-chain dehydrogenase/reductase (SDR)
Function / homologyShort-chain dehydrogenase/reductase SDR / Short-chain dehydrogenase/reductase, conserved site / NAD(P)-binding domain superfamily / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / oxidoreductase activity / 3-oxoacyl-acyl carrier protein reductase
Function and homology information
Specimen sourceLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.302 Å resolution
AuthorsGong, X.M. / Zheng, G.W. / Xu, J.H.
CitationJournal: Acs Catalysis / Year: 2019
Title: Development of an Engineered Ketoreductase with Simultaneously Improved Thermostability and Activity for Making a Bulky Atorvastatin Precursor
Authors: Gong, X.M. / Zhen, Q. / Li, F.L. / Zeng, B.B. / Zheng, G.W. / Xu, J.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 14, 2018 / Release: Jan 16, 2019

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-acyl carrier protein reductase
B: 3-oxoacyl-acyl carrier protein reductase
C: 3-oxoacyl-acyl carrier protein reductase
D: 3-oxoacyl-acyl carrier protein reductase


Theoretical massNumber of molelcules
Total (without water)118,2704
Polyers118,2704
Non-polymers00
Water11,746652
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)12790
ΔGint (kcal/M)-74
Surface area (Å2)33190
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)71.929, 118.194, 248.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: Protein/peptide
3-oxoacyl-acyl carrier protein reductase


Mass: 29567.482 Da / Num. of mol.: 4 / Mutation: M154I,A155D,V198I,A201D,A202L
Source: (gene. exp.) Lactobacillus brevis (strain ATCC 367 / JCM 1170) (bacteria)
Strain: ATCC 367 / JCM 1170 / Gene: LVIS_0330
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q03TH6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Formula: H2O / Water

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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: 2.23 / Density percent sol: 44.81 %
Crystal growTemp: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M MIB buffer (malonic acid:imidazole:boric acid in a mo-lar ratio of 2:3:3) pH 6.0, 21% (v/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRF BEAMLINE BL17U1 / Synchrotron site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Dec 10, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionD resolution high: 2.3 Å / D resolution low: 5 Å / Number obs: 46187 / Rmerge I obs: 0.062 / NetI over sigmaI: 18.906 / Redundancy: 10.2 % / Percent possible obs: 97.6
Reflection shellRmerge I obs: 0.094 / Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefineOverall SU ML: 0.24 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 20.64
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.22 / R factor R work: 0.1681 / R factor obs: 0.1707 / Highest resolution: 2.302 Å / Lowest resolution: 31.006 Å / Number reflection R free: 2320 / Number reflection obs: 46064 / Percent reflection R free: 5.04 / Percent reflection obs: 97.44
Refine hist #LASTHighest resolution: 2.302 Å / Lowest resolution: 31.006 Å
Number of atoms included #LASTProtein: 7320 / Nucleic acid: 0 / Ligand: 0 / Solvent: 652 / Total: 7972
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087416
X-RAY DIFFRACTIONf_angle_d1.05510060
X-RAY DIFFRACTIONf_dihedral_angle_d13.1252656
X-RAY DIFFRACTIONf_chiral_restr0.0731188
X-RAY DIFFRACTIONf_plane_restr0.0041324
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.30200.25630.19622.3490125254498.00
2.34900.25870.18652.4000126259598.00
2.40000.26460.18832.4558134255698.00
2.45580.26080.18602.5172135248596.00
2.51720.25090.19602.5853145252697.00
2.58530.27310.18952.6613129258698.00
2.66130.26540.19432.7471138256899.00
2.74710.22820.18182.8453151255699.00
2.84530.27460.18512.9591136259999.00
2.95910.22860.17593.0937148255998.00
3.09370.21420.18193.2566131261598.00
3.25660.20660.17203.4604126260398.00
3.46040.20990.16053.7272134253296.00
3.72720.21140.15524.1015135245392.00
4.10150.17500.13334.6932148255396.00
4.69320.19600.14625.9062132262197.00
5.90620.16650.145031.0092147279399.00

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