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- PDB-6c49: Crystal Structure of Alcohol Dehydrogenase from Acinetobacter bau... -

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Basic information

Entry
Database: PDB / ID: 6c49
TitleCrystal Structure of Alcohol Dehydrogenase from Acinetobacter baumannii
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Alcohol dehydrogenase / Acinetobacter baumannii / oxidoreductase activity / zinc ion binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / zinc ion binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 ...: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
DI(HYDROXYETHYL)ETHER / Alcohol dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SAD / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Alcohol Dehydrogenase from Acinetobacter baumannii
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,31710
Polymers37,6101
Non-polymers7079
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-24 kcal/mol
Surface area14750 Å2
Unit cell
Length a, b, c (Å)63.440, 89.570, 133.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-588-

HOH

31A-643-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alcohol dehydrogenase


Mass: 37610.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: A7M79_16640, BGC29_12245 / Plasmid: AcbaB.10611.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E3MC83, alcohol dehydrogenase

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Non-polymers , 6 types, 308 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 22.95 mg/mL AcbaB.10611.a.B1.PW38387. For native data crystals: 1:1 protein to JCSG+(g11) (0.1 M Bis-Tris/HCl, pH 5.5, 2 M ammonium sulfate), cryoprotection: 25% ethylene glycol, tray ...Details: 22.95 mg/mL AcbaB.10611.a.B1.PW38387. For native data crystals: 1:1 protein to JCSG+(g11) (0.1 M Bis-Tris/HCl, pH 5.5, 2 M ammonium sulfate), cryoprotection: 25% ethylene glycol, tray 296679g11, puck esb5-1. For anomalous data crystals, 1:1 protein to Morpheus(g3) (10% w/v PEG4000, 20% v/v glycerol, 0.1 M MES/imidazole, pH 6.5, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium), crystal then soaked in same condition + 5% ethylene glycol + 0.25 M sodium iodide for 5 minutes, tray 296680g3, puck esb5-2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 24, 2017
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→44.785 Å / Num. obs: 32531 / % possible obs: 98.9 % / Redundancy: 10.354 % / Biso Wilson estimate: 20.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.057 / Χ2: 0.998 / Net I/σ(I): 29.41 / Num. measured all: 336834 / Scaling rejects: 117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.96.4120.5763.3222450.880.62593.7
1.9-1.956.520.4364.3922500.9250.47395.8
1.95-2.016.70.3255.8522080.9670.35297.2
2.01-2.076.7870.2747.1721830.9720.29798.6
2.07-2.147.4370.2169.8221330.9810.231100
2.14-2.218.8430.1812.9620830.990.191100
2.21-2.299.4710.15615.0720140.9930.165100
2.29-2.399.8760.14616.8319410.9940.154100
2.39-2.4910.5090.1319.2518520.9950.137100
2.49-2.6211.1880.1122.5417800.9970.115100
2.62-2.7612.290.09128.2116970.9980.095100
2.76-2.9314.3890.07436.8915990.9990.077100
2.93-3.1314.5640.05844.4415220.9990.06100
3.13-3.3814.5570.04259.53141110.04499.9
3.38-3.714.5630.03372.46132110.035100
3.7-4.1414.4780.02881.38119310.02999.9
4.14-4.7814.3670.02394.43105710.02499.9
4.78-5.8514.2660.02879.4790310.029100
5.85-8.2713.8530.03276.671610.033100
8.27-44.78512.260.021110.0542310.02298.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.85→44.785 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.2029 2119 6.51 %
Rwork0.1643 --
obs0.1668 32530 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.44 Å2 / Biso mean: 28.4662 Å2 / Biso min: 9.91 Å2
Refinement stepCycle: final / Resolution: 1.85→44.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 37 303 2803
Biso mean--60.62 35.9 -
Num. residues----338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89310.24391260.20941903202994
1.8931-1.94040.25351360.19221915205196
1.9404-1.99290.20211280.18391961208997
1.9929-2.05150.23531370.18322008214598
2.0515-2.11780.22111400.169820322172100
2.1178-2.19340.19491330.175420362169100
2.1934-2.28130.22261570.168619962153100
2.2813-2.38510.21321570.170920312188100
2.3851-2.51080.2471550.175520172172100
2.5108-2.66810.19371430.177220382181100
2.6681-2.87410.20781550.165320452200100
2.8741-3.16320.211440.16420502194100
3.1632-3.62080.17981280.153720882216100
3.6208-4.56110.15351400.140321032243100
4.5611-44.79810.21881400.160421882328100
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)
11.73550.7896-0.12361.5161-0.27821.1283-0.0435-0.0533-0.0606-0.0378-0.0473-0.12540.03920.13260.07090.11580.01730.00320.11450.02860.101813.565212.043139.0444
21.1821-0.60390.77340.8575-0.44692.2739-0.0085-0.05040.22390.0537-0.0774-0.1862-0.19260.31970.07440.2094-0.06690.02470.22410.02040.221214.740713.96766.4167
34.34010.2629-2.57253.3067-0.47724.87780.0681-0.2910.25150.2110.0061-0.0112-0.12340.1618-0.06480.2008-0.04040.00140.14310.0050.182419.10626.871446.2742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 153 )A3 - 153
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 303 )A154 - 303
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 342 )A304 - 342

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