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- PDB-8e7u: F93A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N... -

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Basic information

Entry
Database: PDB / ID: 8e7u
TitleF93A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Ternary complex
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
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 Rossmann-like Domain ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYCLOHEXYLFORMAMIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsZheng, C. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
CitationJournal: To Be Published
Title: Structure of F93A horse liver alcohol dehydrogenase at 1.20 Angstroms resolution
Authors: Zheng, C. / Boxer, S.G.
History
DepositionAug 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,77210
Polymers79,9252
Non-polymers1,8478
Water19,5461085
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.245, 50.771, 92.686
Angle α, β, γ (deg.)92.320, 102.960, 109.310
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 39962.355 Da / Num. of mol.: 2 / Mutation: F93A
Source method: isolated from a genetically manipulated source
Details: liver enzyme / Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-CXF / CYCLOHEXYLFORMAMIDE


Mass: 127.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400 (10%-25%), 2mM NADH, 10mM N-cyclohexylformamide in Tris buffer at pH 8.20

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.19→38.02 Å / Num. obs: 227252 / % possible obs: 97.3 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.031 / Rrim(I) all: 0.119 / Net I/σ(I): 10.2 / Num. measured all: 3069934 / Scaling rejects: 3360
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.19-1.2110.31.268831985850.8010.4041.3261.674.5
6.54-38.0215.80.062229614140.9990.0160.06231.499.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 1.19→38.02 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 16.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1581 11350 5 %
Rwork0.1454 215665 -
obs0.146 227015 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.76 Å2 / Biso mean: 18.2467 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: final / Resolution: 1.19→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 110 1085 6753
Biso mean--12.58 30.11 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.19-1.210.27572510.29384768501965
1.21-1.220.24413680.23297009737795
1.22-1.240.23953810.22387239762098
1.24-1.250.22293830.21477248763198
1.25-1.270.22373820.21887275765798
1.27-1.290.2213780.19567177755597
1.29-1.30.22123770.19087167754497
1.3-1.320.18533800.18037237761798
1.32-1.350.19423850.17657309769498
1.35-1.370.17983790.17097196757598
1.37-1.390.16693860.16277362774899
1.39-1.420.17583850.15537318770399
1.42-1.440.16413820.15187251763399
1.44-1.470.17023840.14547300768498
1.47-1.50.14733760.14247148752497
1.5-1.540.14723850.13937316770198
1.54-1.580.14233840.13267302768698
1.58-1.620.14293830.13017271765499
1.62-1.670.14533860.12597329771599
1.67-1.720.14963860.12857327771399
1.72-1.780.13963830.13737283766699
1.78-1.860.15963820.1397250763298
1.86-1.940.15373830.13547287767098
1.94-2.040.14873860.13687321770799
2.04-2.170.14443870.135573547741100
2.17-2.340.15453860.14017347773399
2.34-2.570.15323830.13947269765298
2.57-2.940.16113840.15087310769498
2.95-3.710.14963890.141473877776100
3.71-38.020.14223860.12757308769499
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)
10.8489-0.4911-0.25781.810.33861.5560.0335-0.10720.02510.1957-0.0121-0.07210.02980.21870.00330.1243-0.0164-0.0310.21240.01370.115722.791-13.908619.6665
20.424-0.0782-0.07990.52680.15570.84920.0094-0.04630.01450.059-0.0191-0.0169-0.03560.099-0.00060.0848-0.0123-0.01020.12070.00420.091317.4555-10.474610.6529
30.77420.0943-0.35890.6966-0.29171.69050.05520.00110.07550.0128-0.03210.0196-0.17590.0668-0.04380.1223-0.0045-0.01050.1139-0.0070.132413.86760.63351.4002
40.210.0795-0.05770.5116-0.05851.22010.0454-0.06010.01810.0827-0.04380.0099-0.04040.0458-0.00460.08-0.005-0.0010.1191-00.101414.4411-8.33688.9993
50.49010.24870.01390.89520.1841.3673-0.03760.0428-0.0704-0.06090.0175-0.00350.1163-0.06280.01720.1044-0.0169-0.01320.1060.00060.10998.4958-26.2112-15.032
60.27270.0295-0.17010.42380.05191.02630.0118-0.00410.0103-0.08950.017-0.0082-0.0088-0.0210.00560.0864-0.0085-0.01460.09690.00430.098513.3888-14.4852-12.8813
70.75470.07430.08810.61010.13311.44450.0566-0.0659-0.0550.0855-0.0107-0.02120.1617-0.0560.01940.1392-0.0114-0.0110.12680.01470.127111.5059-25.34349.9648
81.43410.2640.29750.81480.13291.5383-0.11540.1685-0.16-0.23390.081-0.12050.07360.09040.01630.26370.02830.10010.1638-0.00020.172128.9363-16.4076-60.1072
90.60480.15140.11910.49880.07650.9666-0.05780.0773-0.0627-0.12330.0212-0.02730.1358-0.00080.00750.18910.00510.03940.12250.00340.106322.0092-13.0502-52.0973
100.76290.2451-0.1130.5106-0.0931.3898-0.05520.1109-0.0317-0.12650.0140.04560.1791-0.2635-0.03820.1984-0.0328-0.00340.1795-0.01280.1137.3893-12.8481-52.0696
111.0418-0.0207-0.76930.63310.10891.9309-0.10620.002-0.026-0.03820.0523-0.12130.3417-0.01840.05230.2105-0.00770.02390.11230.0040.121616.6455-20.6601-45.5081
120.36140.1746-0.08910.51080.00591.0637-0.04210.07510.0301-0.13680.0261-0.03930.0505-0.019-0.00230.15960.0020.00850.12410.01180.100116.8044-6.358-49.4064
130.64950.2599-0.04760.71770.21061.27290.0109-0.01330.05270.0253-0.018-0.0517-0.07560.0863-0.00040.1199-0.00670.00330.10170.0020.128127.29624.7789-26.9208
140.34090.1097-0.00090.223-0.04921.10440.0050.01420.0181-0.0563-0.0117-0.04410.00730.04490.01340.12630.00370.01410.08890.00150.114923.7618-3.8247-36.1392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )A1 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 76 )A29 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 119 )A77 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 184 )A120 - 184
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 271 )A185 - 271
6X-RAY DIFFRACTION6chain 'A' and (resid 272 through 342 )A272 - 342
7X-RAY DIFFRACTION7chain 'A' and (resid 343 through 374 )A343 - 374
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 28 )B1 - 28
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 76 )B29 - 76
10X-RAY DIFFRACTION10chain 'B' and (resid 77 through 100 )B77 - 100
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 137 )B101 - 137
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 184 )B138 - 184
13X-RAY DIFFRACTION13chain 'B' and (resid 185 through 271 )B185 - 271
14X-RAY DIFFRACTION14chain 'B' and (resid 272 through 374 )B272 - 374

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