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- PDB-8za3: lbADH mutant A144F with NADP -

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Basic information

Entry
Database: PDB / ID: 8za3
TitlelbADH mutant A144F with NADP
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / rational design
Function / homology
Function and homology information


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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLevilactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsXu, W.H. / Cen, Y.X. / Wu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: lbADH mutant A144F 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

Downloads & links

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Assembly

Deposited unit
A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7226
Polymers26,6741
Non-polymers1,0485
Water3,585199
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)110,89024
Polymers106,6964
Non-polymers4,19320
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 area20980 Å2
ΔGint-126 kcal/mol
Surface area31580 Å2
MethodPISA
2
A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,44512
Polymers53,3482
Non-polymers2,09710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6450 Å2
ΔGint-36 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.900, 82.360, 112.640
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-303-

MG

21A-537-

HOH

31A-575-

HOH

41A-581-

HOH

51A-582-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein R-specific alcohol dehydrogenase


Mass: 26674.121 Da / Num. of mol.: 1 / Mutation: E144F
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 , 5 types, 204 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 30% PEG1000 0.1 M Tris pH 8.5

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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: 1.56→46.25 Å / Num. obs: 36446 / % possible obs: 97.5 % / Redundancy: 10.5 % / Biso Wilson estimate: 16.72 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.7
Reflection shellResolution: 1.56→1.59 Å / Num. unique obs: 1464 / CC1/2: 0.882

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→26.67 Å / SU ML: 0.1359 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1879 1831 5.03 %
Rwork0.1627 34574 -
obs0.1639 36405 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.3 Å2
Refinement stepCycle: LAST / Resolution: 1.56→26.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 67 199 2139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841994
X-RAY DIFFRACTIONf_angle_d0.9392701
X-RAY DIFFRACTIONf_chiral_restr0.0599306
X-RAY DIFFRACTIONf_plane_restr0.0063344
X-RAY DIFFRACTIONf_dihedral_angle_d17.2987746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.25161050.22132240X-RAY DIFFRACTION82.89
1.6-1.650.20981270.18692464X-RAY DIFFRACTION91.72
1.65-1.70.20551500.15622621X-RAY DIFFRACTION96.96
1.7-1.760.18021330.1552684X-RAY DIFFRACTION99.82
1.76-1.830.16351420.15812717X-RAY DIFFRACTION99.97
1.83-1.920.24491490.20212656X-RAY DIFFRACTION98.32
1.92-2.020.22661400.18042663X-RAY DIFFRACTION98.42
2.02-2.140.22371560.17612711X-RAY DIFFRACTION99.34
2.14-2.310.19911360.16892661X-RAY DIFFRACTION98.31
2.31-2.540.16271590.15262721X-RAY DIFFRACTION100
2.54-2.910.18551640.15522733X-RAY DIFFRACTION99.93
2.91-3.670.18741460.15412776X-RAY DIFFRACTION99.93
3.67-26.670.15181240.15382927X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -25.1154674252 Å / Origin y: -15.6228146679 Å / Origin z: -14.6881414064 Å
111213212223313233
T0.161190668022 Å20.00930849720202 Å20.00396274351043 Å2-0.160267512125 Å2-0.0214989516235 Å2--0.152855978295 Å2
L0.65552137895 °20.0179814620635 °20.0795531118758 °2-0.523818831783 °20.056886922702 °2--0.542711606898 °2
S0.0204563634493 Å °0.0845346519545 Å °-0.119093808676 Å °-0.0833064009984 Å °-0.0138834576232 Å °-0.0283809095664 Å °0.0755514692968 Å °0.031957379823 Å °-0.0113383762203 Å °
Refinement TLS groupSelection details: all

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