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- PDB-7xl5: Crystal structure of the H42T/A85G/I86A mutant of a nadp-dependen... -

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Basic information

Entry
Database: PDB / ID: 7xl5
TitleCrystal structure of the H42T/A85G/I86A mutant of a nadp-dependent alcohol dehydrogenase
ComponentsNADP-dependent isopropanol dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / mutant / Thermoanaerobacter brockii
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter brockii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsJiang, Y.Y. / Qu, G. / Li, X. / Sun, Z.T. / Han, X. / Liu, W.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the H42T/A85G/I86A mutant of a nadp-dependent alcohol dehydrogenase
Authors: Jiang, Y.Y. / Qu, G. / Li, X. / Sun, Z.T. / Han, X. / Liu, W.D.
History
DepositionApr 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent isopropanol dehydrogenase
B: NADP-dependent isopropanol dehydrogenase
C: NADP-dependent isopropanol dehydrogenase
D: NADP-dependent isopropanol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)153,7224
Polymers153,7224
Non-polymers00
Water6,053336
1
B: NADP-dependent isopropanol dehydrogenase
C: NADP-dependent isopropanol dehydrogenase

A: NADP-dependent isopropanol dehydrogenase

D: NADP-dependent isopropanol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)153,7224
Polymers153,7224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation3_745-x+2,y-1/2,-z+1/21
Buried area14500 Å2
ΔGint-82 kcal/mol
Surface area46310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.550, 130.867, 134.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 0 through 351)
21(chain B and resid 0 through 351)
31(chain C and resid 1 through 351)
41(chain D and resid 0 through 351)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA0 - 3516 - 357
2chain BBB0 - 3516 - 357
3(chain C and resid 1 through 351)CC1 - 3517 - 357
4chain DDD0 - 3516 - 357

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Components

#1: Protein
NADP-dependent isopropanol dehydrogenase


Mass: 38430.602 Da / Num. of mol.: 4 / Mutation: H42T, A85G, I86A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Gene: adh / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14941, isopropanol dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium acetate tetrahydrate, 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.604→47.3 Å / Num. obs: 43076 / % possible obs: 98.73 % / Redundancy: 6.4 % / Biso Wilson estimate: 33.7 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.83
Reflection shellResolution: 2.604→2.697 Å / Num. unique obs: 3863 / CC1/2: 0.865

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YKF

1ykf


Resolution: 2.604→47.3 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 2162 5.02 %
Rwork0.1857 40908 -
obs0.1877 43070 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.01 Å2 / Biso mean: 37.2201 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 2.604→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10564 0 0 336 10900
Biso mean---34.75 -
Num. residues----1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610754
X-RAY DIFFRACTIONf_angle_d0.99614553
X-RAY DIFFRACTIONf_chiral_restr0.0591625
X-RAY DIFFRACTIONf_plane_restr0.0061890
X-RAY DIFFRACTIONf_dihedral_angle_d7.0936412
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6605X-RAY DIFFRACTION12.45TORSIONAL
12B6605X-RAY DIFFRACTION12.45TORSIONAL
13C6605X-RAY DIFFRACTION12.45TORSIONAL
14D6605X-RAY DIFFRACTION12.45TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.604-2.66450.2561220.2471235787
2.6645-2.73110.34281810.246263798
2.7311-2.80490.27621310.2393264498
2.8049-2.88750.27221360.2361273199
2.8875-2.98070.29511460.24342722100
2.9807-3.08720.2851340.23072723100
3.0872-3.21070.2761500.22552736100
3.2107-3.35680.26891460.20552741100
3.3568-3.53380.22471360.18472760100
3.5338-3.75510.19291390.17912754100
3.7551-4.04490.21450.16322758100
4.0449-4.45160.17741550.142779100
4.4516-5.09510.17781450.14282781100
5.0951-6.41680.2031360.16712832100
6.4168-47.30.19561600.16732953100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29630.8086-1.05412.2246-1.02543.07380.2888-0.19470.42060.41180.07760.098-0.79570.128-0.27680.3397-0.03650.04170.3027-0.0570.247327.3247171.869441.7049
21.63920.18470.01070.64890.09842.97640.0651-0.1501-0.01120.15010.0316-0.05110.0690.2424-0.10110.14260.0214-0.00410.2050.03490.181120.9175156.700335.0909
32.3192-0.1982-0.29780.88880.11461.4160.06280.360.1907-0.1007-0.01740.0144-0.19840.0225-0.01020.1625-0.02330.00370.19750.04550.20758.9633160.472920.0557
42.5120.6302-0.38743.87410.04151.85810.0589-0.02790.306-0.06560.0812-0.1811-0.23690.4332-0.21870.1433-0.0489-0.0080.39390.02860.206433.0102163.890827.739
51.6815-1.3338-0.93672.94831.54992.04540.2290.42720.3036-0.6961-0.0347-0.3768-0.5507-0.2291-0.14870.34510.00520.05150.39220.09590.250852.3924160.25867.4027
62.08760.3582-0.23493.21321.72453.36770.001-0.0809-0.63550.1621-0.21990.04170.5737-0.60390.17870.247-0.0739-0.00680.2867-0.01890.334749.9223140.873411.2844
73.219-1.0184-0.58931.78091.1143.04520.04370.1983-0.0528-0.1628-0.0577-0.10550.04350.06550.00060.1957-0.0340.01350.15030.02590.171858.5101149.548914.9751
80.89321.20350.36112.02281.31495.48520.0648-0.0713-0.03440.11580.0169-0.05930.37840.1466-0.0440.11180.0080.00490.0851-0.00690.1566.2772156.979333.1785
93.88490.03990.19261.33260.28472.6707-0.0278-0.13440.4719-0.06-0.0401-0.0783-0.3413-0.1010.01460.17960.00510.01470.09990.00960.253565.8346166.194936.491
102.04010.42880.29180.72140.04671.3221-0.16020.09080.2204-0.20860.04480.0375-0.09160.14770.01640.18440.0023-0.02930.20220.01160.201471.1163158.398926.7296
112.7996-0.72940.49132.3105-0.51351.20810.07740.07490.06330.2228-0.01230.44140.0168-0.4041-0.00960.165-0.0792-0.02190.3167-0.02950.204946.7935155.8428.5959
122.2763-0.8878-1.66624.3086-1.05265.5264-0.06530.35170.6917-0.3836-0.10490.0414-0.7427-0.31190.05660.21020.05470.02250.30750.06960.255146.6107167.000520.1543
132.57040.9095-0.47051.6314-1.0292.12610.1004-0.4187-0.41320.2325-0.171-0.08510.00170.10650.0450.3181-0.069-0.02390.25740.06260.260580.8601144.776863.3811
142.6082-0.3241-0.78491.41230.08312.38070.09130.0442-0.34150.0536-0.0669-0.01040.4613-0.08450.01840.2983-0.069-0.03950.15590.04230.257966.4341132.064741.0631
151.42570.00740.14641.4753-0.95791.5404-0.0062-0.2383-0.11240.19080.05310.0388-0.027-0.2215-0.11390.327-0.08180.03750.29150.02420.229866.9163142.959960.6702
161.31751.898-0.29683.1066-0.42390.38450.2777-0.2972-0.60780.3965-0.4564-0.36020.4415-0.1953-0.11930.508-0.0266-0.02940.29120.11170.584482.8232181.324665.0503
172.60850.6231-0.19771.4687-0.25151.4048-0.0601-0.1942-0.4435-0.07620.16-0.05430.20640.0652-0.01450.2811-0.0017-0.02210.27740.05890.293781.7452192.557257.9767
181.9636-0.19370.88430.4905-0.25291.6995-0.0467-0.1871-0.2397-0.00920.09140.13870.2214-0.3112-0.07850.2326-0.07050.01110.20050.03380.301468.4725196.735550.5684
190.8502-0.175-0.4780.446-0.12580.391-0.04310.524-0.6429-0.46040.09390.16110.698-0.3907-0.06860.4219-0.1552-0.09050.2869-0.09410.421759.7785192.648730.7654
202.0297-0.4079-0.72041.63210.49333.0942-0.10640.212-0.435-0.3114-0.0603-0.04490.2306-0.1661-0.01590.3629-0.0221-0.03570.2512-0.0440.360674.2759192.351529.0387
211.26030.2844-0.11580.4922-0.28222.46180.2699-0.1956-0.14650.03280.0030.36650.359-0.0742-0.09220.2626-0.01030.02110.29470.05780.24673.5122203.90554.6773
220.33610.4378-0.31610.6189-0.1181.9985-0.0594-0.5218-0.36720.32850.0510.40890.3037-0.5339-0.12480.2737-0.08990.05290.380.14120.334160.7234195.030458.1589
231.3845-0.2791-0.71261.5882-0.81942.06-0.189-0.359-0.46940.1764-0.09550.13540.6054-0.2463-0.10760.409-0.13830.05920.27020.20590.602465.4112180.825958.2542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 60 )A1 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 210 )A61 - 210
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 310 )A211 - 310
4X-RAY DIFFRACTION4chain 'A' and (resid 311 through 351 )A311 - 351
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 59 )B1 - 59
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 79 )B60 - 79
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 150 )B80 - 150
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 176 )B151 - 176
9X-RAY DIFFRACTION9chain 'B' and (resid 177 through 269 )B177 - 269
10X-RAY DIFFRACTION10chain 'B' and (resid 270 through 310 )B270 - 310
11X-RAY DIFFRACTION11chain 'B' and (resid 311 through 327 )B311 - 327
12X-RAY DIFFRACTION12chain 'B' and (resid 328 through 351 )B328 - 351
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 150 )C1 - 150
14X-RAY DIFFRACTION14chain 'C' and (resid 151 through 292 )C151 - 292
15X-RAY DIFFRACTION15chain 'C' and (resid 293 through 352 )C293 - 352
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 26 )D1 - 26
17X-RAY DIFFRACTION17chain 'D' and (resid 27 through 112 )D27 - 112
18X-RAY DIFFRACTION18chain 'D' and (resid 113 through 210 )D113 - 210
19X-RAY DIFFRACTION19chain 'D' and (resid 211 through 245 )D211 - 245
20X-RAY DIFFRACTION20chain 'D' and (resid 246 through 292 )D246 - 292
21X-RAY DIFFRACTION21chain 'D' and (resid 293 through 310 )D293 - 310
22X-RAY DIFFRACTION22chain 'D' and (resid 311 through 326 )D311 - 326
23X-RAY DIFFRACTION23chain 'D' and (resid 327 through 351 )D327 - 351

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