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- PDB-8za2: lbADH mutant L195S/V196L with NADP -

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Basic information

Entry
Database: PDB / ID: 8za2
TitlelbADH mutant L195S/V196L 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLevilactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsXu, W.H. / Cen, Y.X. / Wu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: lbADH mutant L195S/V196L 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
B: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,78416
Polymers53,2882
Non-polymers2,49614
Water1,802100
1
A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,13664
Polymers213,1528
Non-polymers9,98456
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_544y+1/2,x-1/2,-z-1/21
crystal symmetry operation10_545-x,-y-1,z1
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area44680 Å2
ΔGint-503 kcal/mol
Surface area64170 Å2
MethodPISA
2
A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,56832
Polymers106,5764
Non-polymers4,99228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area21640 Å2
ΔGint-234 kcal/mol
Surface area32780 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-91 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.670, 188.670, 128.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-306-

MG

21A-401-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLNGLNchain 'A'AA1 - 2511 - 251
12NAPNAPNAPNAPchain 'A'AC301
21SERSERGLNGLNchain 'B'BB1 - 2511 - 251
22NAPNAPNAPNAPchain 'B'BK301

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Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 26644.008 Da / Num. of mol.: 2 / Mutation: L195S, V196L
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
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
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: 5.34 Å3/Da / Density % sol: 76.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate 0.1 M Tirs pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.03845 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03845 Å / Relative weight: 1
ReflectionResolution: 2.78→48.47 Å / Num. obs: 29417 / % possible obs: 100 % / Redundancy: 25.8 % / Biso Wilson estimate: 44.51 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.2
Reflection shellResolution: 2.78→2.93 Å / Num. unique obs: 4249 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→43.74 Å / SU ML: 0.2994 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 1511 5.14 %
Rwork0.1866 27889 -
obs0.188 29400 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.24 Å2
Refinement stepCycle: LAST / Resolution: 2.78→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 148 100 3988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273946
X-RAY DIFFRACTIONf_angle_d0.53055360
X-RAY DIFFRACTIONf_chiral_restr0.0441604
X-RAY DIFFRACTIONf_plane_restr0.0043678
X-RAY DIFFRACTIONf_dihedral_angle_d17.92061452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.870.31951450.27922482X-RAY DIFFRACTION100
2.87-2.970.26451350.26572500X-RAY DIFFRACTION100
2.97-3.090.30851510.25352503X-RAY DIFFRACTION100
3.09-3.230.27021290.24512491X-RAY DIFFRACTION100
3.23-3.40.24681320.2212513X-RAY DIFFRACTION100
3.4-3.620.22881410.19812521X-RAY DIFFRACTION100
3.62-3.890.16991410.17442518X-RAY DIFFRACTION99.96
3.89-4.290.19181180.15512544X-RAY DIFFRACTION100
4.29-4.910.17131350.14432550X-RAY DIFFRACTION99.96
4.91-6.180.18511400.15792576X-RAY DIFFRACTION100
6.18-43.740.18311440.15932691X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -14.166 Å / Origin y: -61.736 Å / Origin z: -23.477 Å
111213212223313233
T0.285616153223 Å2-0.0197100411334 Å2-0.0229906037622 Å2-0.309618901351 Å2-0.0168981227597 Å2--0.289130853725 Å2
L0.886545650038 °2-0.397623944848 °20.0347236294908 °2-1.0097213466 °2-0.131931726649 °2--0.623134586207 °2
S0.0235217844549 Å °-0.0827027972391 Å °0.0864017252265 Å °0.0583668760447 Å °-0.00872244593089 Å °-0.151004148059 Å °-0.0301483563472 Å °0.159642866532 Å °-0.0135157730032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )A1 - 251
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )A301
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )A302 - 307
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )A401 - 461
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )A308
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )B1 - 251
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )B301
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )B302 - 305
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )B401 - 439
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:307 OR RESID 401:461 OR RESID 308:308 ) ) OR ( CHAIN B AND ( RESID 1:251 OR RESID 301:301 OR RESID 302:305 OR RESID 401:439 OR RESID 306:306 ) )B306

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