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- PDB-5zfm: Ketoreductase LbCR mutant - M6 -

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Basic information

Entry
Database: PDB / ID: 5zfm
TitleKetoreductase LbCR mutant - M6
Components3-oxoacyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / ketoreductase / short-chain dehydrogenase/reductase (SDR)
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
3-oxoacyl-acyl carrier protein reductase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGong, X.M. / Zheng, G.W. / Xu, J.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21472045 China
National Natural Science Foundation of China21536004 China
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.
History
DepositionMar 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 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)118,2144
Polymers118,2144
Non-polymers00
Water21,3301184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-81 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.338, 116.052, 75.183
Angle α, β, γ (deg.)90.00, 114.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29553.455 Da / Num. of mol.: 4 / Mutation: M154A,A155D,A201D,A202L
Source method: isolated from a genetically manipulated source
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 / Water


Mass: 18.015 Da / Num. of mol.: 1184 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, MES buffer, sodium chloride, glycyl-glycyl-glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2→44.28 Å / Num. obs: 72544 / % possible obs: 99.08 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 10.143
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.516

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.278 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.1946 3657 5.05 %
Rwork0.1584 --
obs0.1602 72443 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→44.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7316 0 0 1184 8500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087412
X-RAY DIFFRACTIONf_angle_d0.99510056
X-RAY DIFFRACTIONf_dihedral_angle_d12.0112652
X-RAY DIFFRACTIONf_chiral_restr0.0691188
X-RAY DIFFRACTIONf_plane_restr0.0041324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.02640.2511210.2012235X-RAY DIFFRACTION84
2.0264-2.05410.26291390.18922642X-RAY DIFFRACTION100
2.0541-2.08350.23161490.1872631X-RAY DIFFRACTION100
2.0835-2.11460.21121570.17752629X-RAY DIFFRACTION100
2.1146-2.14760.21781370.16452659X-RAY DIFFRACTION100
2.1476-2.18280.23521330.17322680X-RAY DIFFRACTION100
2.1828-2.22050.20551290.17322656X-RAY DIFFRACTION100
2.2205-2.26080.22621510.16832652X-RAY DIFFRACTION100
2.2608-2.30430.23671390.16332677X-RAY DIFFRACTION100
2.3043-2.35140.19961350.16312616X-RAY DIFFRACTION100
2.3514-2.40250.23671530.17472652X-RAY DIFFRACTION100
2.4025-2.45840.2441420.17482677X-RAY DIFFRACTION100
2.4584-2.51980.23161350.17952640X-RAY DIFFRACTION100
2.5198-2.5880.20391530.17542672X-RAY DIFFRACTION100
2.588-2.66410.19491250.16372654X-RAY DIFFRACTION100
2.6641-2.75010.21811410.17792663X-RAY DIFFRACTION100
2.7501-2.84840.22511260.16982647X-RAY DIFFRACTION100
2.8484-2.96240.23821370.17172679X-RAY DIFFRACTION100
2.9624-3.09720.19611560.17352659X-RAY DIFFRACTION100
3.0972-3.26040.17551340.16032695X-RAY DIFFRACTION100
3.2604-3.46460.1881310.15372664X-RAY DIFFRACTION100
3.4646-3.7320.17221660.14262665X-RAY DIFFRACTION100
3.732-4.10730.15381490.13542660X-RAY DIFFRACTION100
4.1073-4.70110.15481500.12482665X-RAY DIFFRACTION100
4.7011-5.92060.17521340.1482693X-RAY DIFFRACTION100
5.9206-44.28850.17841350.1542724X-RAY DIFFRACTION99

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