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- PDB-6zdz: Tetragonal crystal structure of the bulky-bulky ketone specific a... -

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Basic information

Entry
Database: PDB / ID: 6zdz
TitleTetragonal crystal structure of the bulky-bulky ketone specific alcohol dehydrogenase from Comamonas testosteroni
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / bulky-bulky ketones / NADPH-dependent
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Short-subunit dehydrogenase
Function and homology information
Biological speciesComamonas sp. 26 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsToelzer, C. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB635/project B07 Germany
CitationJournal: Catalysts / Year: 2020
Title: Expanding the Application Range of Microbial Oxidoreductases by an Alcohol Dehydrogenase from Comamonas testosteroni with a Broad Substrate Spectrum and pH Profile
Authors: Bakonyi, D. / Toelzer, C. / Stricker, M. / Hummel, W. / Niefind, K. / Groger, H.
History
DepositionJun 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2444
Polymers59,0512
Non-polymers1922
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-78 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.481, 103.481, 112.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 76 or resid 78 through 185 or resid 202 through 259))
d_2ens_1(chain "B" and (resid 2 through 76 or resid 78 through 259))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRLEUA1 - 75
d_12ens_1GLUALAA78 - 185
d_13ens_1PROLEUA187 - 244
d_21ens_1THRLEUB1 - 75
d_22ens_1GLULEUB77 - 242

NCS oper: (Code: givenMatrix: (0.97685288174, -0.213905748249, 0.00166682375098), (-0.213904469847, -0.976854157181, -0.000912894939528), (0.00182351718554, 0.000535223001622, -0.999998194159)Vector: ...NCS oper: (Code: given
Matrix: (0.97685288174, -0.213905748249, 0.00166682375098), (-0.213904469847, -0.976854157181, -0.000912894939528), (0.00182351718554, 0.000535223001622, -0.999998194159)
Vector: 10.9945071887, 102.327206616, 79.9404127338)

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Components

#1: Protein alcohol dehydrogenase


Mass: 29525.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas sp. 26 (bacteria) / Gene: CLU84_2013 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G6ZQ46
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 % polyethylene glycol 4000, 0.2 M magnesium chloride, 60 mM potassium sulphate, 0.1 M MES buffer, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.153→76.153 Å / Num. obs: 23618 / % possible obs: 70.1 % / Redundancy: 25.3 % / Biso Wilson estimate: 39.65 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.2
Reflection shellResolution: 2.153→2.361 Å / Redundancy: 24.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1182 / CC1/2: 0.68 / % possible all: 14.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMV

4bmv


Resolution: 2.153→51.74 Å / SU ML: 0.2315 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 1173 4.97 %
Rwork0.1906 22427 -
obs0.1925 23600 70.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.39 Å2
Refinement stepCycle: LAST / Resolution: 2.153→51.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 10 166 3855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173743
X-RAY DIFFRACTIONf_angle_d0.43885069
X-RAY DIFFRACTIONf_chiral_restr0.04603
X-RAY DIFFRACTIONf_plane_restr0.0033662
X-RAY DIFFRACTIONf_dihedral_angle_d15.04681387
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.718714757352 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.250.3736160.3263296X-RAY DIFFRACTION7.56
2.25-2.370.3829480.3083894X-RAY DIFFRACTION22.93
2.37-2.520.2832800.27741632X-RAY DIFFRACTION41.07
2.52-2.710.27681680.27533352X-RAY DIFFRACTION84.39
2.71-2.980.28352070.24063980X-RAY DIFFRACTION100
2.98-3.420.25992110.20323995X-RAY DIFFRACTION100
3.42-4.30.20622100.16534051X-RAY DIFFRACTION99.77
4.3-51.740.19152330.15764227X-RAY DIFFRACTION99.89
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)
12.79142942072-0.233658217851.385790561370.1361653715930.2176728918821.652726747160.06356921256230.501302030112-0.61273505452-0.126142935281-0.239803024979-0.5553702612980.5513175872930.246766299183-0.1624239185990.5045749938470.1937435429350.1156982961830.2898610715720.03705262476150.47427288111212.568564800334.821713100720.8873438431
21.341247214610.3274677161650.5186457639050.8190349275070.3721135658791.012580590330.001615064010910.434396774631-0.324468935048-0.5015750278-0.0664306909863-0.4173543473770.6664824476420.4140142440130.0158260047750.474329323130.1453626619070.1187057587230.360326641130.02564690628430.2730336057913.591168551639.031044277516.9914585896
31.66354933636-0.723382944992-0.09419152537852.00070688811-0.05478943404671.30262682918-0.09380522773150.208640669124-0.173738236641-0.108420214755-0.03897379502550.07508524080860.544160058937-0.2562886370160.1151523715830.4426607812280.008558112665840.06953736663960.257189186993-0.002161637868730.2530550915225.5489198491938.80261225921.8206552581
40.3915389953190.4742592548530.5265980614853.812398296391.495222958321.287153913210.2024427542820.3007536151880.562833294993-0.864846344307-0.353765408565-0.600499629026-0.331798172890.01201823886510.1448996850830.2980150163270.03017240858470.002125230235020.2622586651250.1131423129110.40700170204512.616495830157.60989278733.1082893606
51.410969551930.288449858025-0.2418011488120.226852768984-0.2184037689892.84640416456-0.01163941300010.0508174457619-0.185249416787-0.226873780272-0.113145366206-0.2262454938430.7246860922450.41859908480.0920791792720.2159289367870.136736147880.08541399142940.3545686542650.1107894278090.32486470223219.298686923141.187781996734.7708729759
63.102595048130.3358507097781.454164228130.9355450210250.6197543523950.918726543452-0.05797387437560.736502599795-0.209240408447-0.742198802005-0.108213380052-0.8156230297520.4068483619260.8849987724410.07540944168160.512527085870.2565177498340.1636533185950.6233931919610.1339653374450.49893254398427.637709107641.834040096722.9028876474
71.815031531880.0748407527244-1.167618918792.378243108341.659615910881.975904487990.106977015712-0.256667250941-0.2525264566850.343723951606-0.0528412073318-0.5005540517110.7169378199080.996371652188-0.1673071182570.3470356189940.209698471428-0.0308203330680.770362029690.2152824724660.64938494563736.490756790945.68686677348.3658996605
83.78568520367-0.4583076836110.4676316410770.0560817376932-0.0003151366671383.563059722520.105012911968-0.03107310110580.4334833256120.356544502982-0.329634078075-0.213249642771-0.4961182942730.1932684073190.1645869570680.426437026064-0.0621761818507-0.06691863045340.2767820737270.05619975223710.3669976367915.39362196265.699816430659.2704879681
92.435112006960.632852277987-0.9038380174821.76183032796-0.516449069362.17063563967-0.069820138186-0.2009269101860.2117729114240.326387229343-0.0977416118795-0.0383801649553-0.5496597958670.07078842102510.1549855801620.314120369877-0.0229384007323-0.06513074017590.1731006657340.02074228003670.2356194839110.644824279862.49676251259.8760939355
100.5443412792450.1102017751830.1155304269082.531194109331.542863874160.949597699960.0775269650268-0.266033709122-0.2155064642940.260701305052-0.435757352946-0.4625784556790.3129666801980.2125347731070.1725124056040.293713211640.08046979443290.009756747370370.2588430200610.1204158918660.38659072619811.037547510243.329605684946.8505291988
111.19577935361-0.260156489789-0.2481931737161.574794198860.532415980091.583385894120.06572028172370.127689155776-0.07729788724860.0426568726775-0.251908873781-0.586611054729-0.03989974376230.935278140476-0.1251042146710.1283741397110.0112725877671-0.02513076209670.4052148469640.1951051765340.32424794888327.464312216155.300913864545.6981897703
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 14 )AA2 - 141 - 13
22chain 'A' and (resid 15 through 37 )AA15 - 3714 - 36
33chain 'A' and (resid 38 through 87 )AA38 - 8737 - 87
44chain 'A' and (resid 88 through 113 )AA88 - 11388 - 113
55chain 'A' and (resid 114 through 174 )AA114 - 174114 - 174
66chain 'A' and (resid 175 through 231 )AA175 - 231175 - 216
77chain 'A' and (resid 232 through 259 )AA232 - 259217 - 244
88chain 'B' and (resid 2 through 14 )BB2 - 141 - 13
99chain 'B' and (resid 15 through 87 )BB15 - 8714 - 86
1010chain 'B' and (resid 88 through 113 )BB88 - 11387 - 112
1111chain 'B' and (resid 114 through 259 )BB114 - 259113 - 242

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