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- PDB-8za1: lbADH mutant E144R with NADP -

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Basic information

Entry
Database: PDB / ID: 8za1
TitlelbADH mutant E144R with NADP
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / rational design
Function / homology
Function and homology information


bile acid metabolic process / oxidoreductase activity / nucleotide binding / metal ion binding
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 domain superfamily
Similarity search - Domain/homology
ACETIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLevilactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXu, W.H. / Cen, Y.X. / Wu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: lbADH mutant E144R with NADP
Authors: Xu, W.H. / Cen, Y.X. / Wu, Q.
History
DepositionApr 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,19112
Polymers26,6841
Non-polymers1,50711
Water2,990166
1
A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,76448
Polymers106,7374
Non-polymers6,02744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area23670 Å2
ΔGint-81 kcal/mol
Surface area32020 Å2
MethodPISA
2
A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38224
Polymers53,3682
Non-polymers3,01422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7380 Å2
ΔGint-18 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.710, 82.510, 113.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-310-

MG

21A-414-

HOH

31A-508-

HOH

41A-509-

HOH

51A-526-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein R-specific alcohol dehydrogenase


Mass: 26684.141 Da / Num. of mol.: 1 / Mutation: E144R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Levilactobacillus brevis (bacteria) / Gene: radh / Production host: Escherichia coli (E. coli) / References: UniProt: Q84EX5

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Non-polymers , 7 types, 177 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H4O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 30% PEG400 0.2 M MgCl2 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.6→33.33 Å / Num. obs: 34777 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1705 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.86 Å / SU ML: 0.1542 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.6645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1654 1736 4.99 %
Rwork0.1489 33020 -
obs0.1497 34756 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.76 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 97 166 2136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882030
X-RAY DIFFRACTIONf_angle_d0.97822738
X-RAY DIFFRACTIONf_chiral_restr0.0689307
X-RAY DIFFRACTIONf_plane_restr0.0061349
X-RAY DIFFRACTIONf_dihedral_angle_d15.3459766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.26731670.2322677X-RAY DIFFRACTION99.96
1.65-1.70.23081440.20392703X-RAY DIFFRACTION99.86
1.7-1.760.23941370.18112732X-RAY DIFFRACTION100
1.76-1.830.21581620.16742709X-RAY DIFFRACTION99.86
1.83-1.910.17591360.14482730X-RAY DIFFRACTION99.93
1.91-2.020.17621470.13522725X-RAY DIFFRACTION99.97
2.02-2.140.18231160.13472774X-RAY DIFFRACTION100
2.14-2.310.15371580.12992719X-RAY DIFFRACTION99.97
2.31-2.540.16491300.14032766X-RAY DIFFRACTION99.97
2.54-2.910.17131430.14862782X-RAY DIFFRACTION100
2.91-3.660.13181330.14512802X-RAY DIFFRACTION99.97
3.66-27.860.15391630.14972901X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: -25.1022279622 Å / Origin y: -15.4342750747 Å / Origin z: -14.7918905284 Å
111213212223313233
T0.211051100491 Å20.0125563146952 Å20.00953865106785 Å2-0.212230354412 Å2-0.0238615367267 Å2--0.206970637184 Å2
L0.721766524173 °20.0736083991684 °20.00848247825845 °2-0.783362762151 °20.146194436543 °2--0.84924694831 °2
S0.00214000868814 Å °0.118181557239 Å °-0.143025594443 Å °-0.0974704215247 Å °-0.0105540241086 Å °-0.0408707076377 Å °0.09575259799 Å °0.0355653470414 Å °0.00567871249727 Å °
Refinement TLS groupSelection details: all

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