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- PDB-6ze0: Orthorhombic crystal structure of the bulky-bulky ketone specific... -

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Basic information

Entry
Database: PDB / ID: 6ze0
TitleOrthorhombic 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: 1.99 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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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
C: alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)88,5773
Polymers88,5773
Non-polymers00
Water8,071448
1
A: alcohol dehydrogenase
B: alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)59,0512
Polymers59,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: alcohol dehydrogenase

C: alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)59,0512
Polymers59,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)49.929, 70.820, 210.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-472-

HOH

21C-481-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 39 or resid 41 through 106 or resid 108 through 260))
d_2ens_1(chain "B" and (resid 2 through 39 or resid 41...
d_3ens_1(chain "C" and (resid 2 through 39 or resid 41...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRVALA1 - 38
d_12ens_1METASPA40 - 105
d_13ens_1LEUPROA107 - 249
d_21ens_1THRVALB1 - 38
d_22ens_1METASPB41 - 106
d_23ens_1LEUTHRB108 - 188
d_24ens_1ASNPROB190 - 251
d_31ens_1THRVALC1 - 38
d_32ens_1METASPC40 - 105
d_33ens_1LEUTHRC108 - 188
d_34ens_1ASNPROC191 - 252

NCS oper:
IDCodeMatrixVector
1given(0.964238173574, -0.130531532557, 0.230664829634), (-0.129674156743, -0.991375736865, -0.0189409986), (0.231147913023, -0.0116476333773, -0.972848896254)-10.5789375529, 78.3410133767, 133.687480101
2given(-0.991466813049, 0.0561224691335, -0.117659793815), (-0.0575906377374, -0.998298689775, 0.00911287213205), (-0.116948181119, 0.0158112128523, 0.993012149211)99.1044693715, 37.5940598657, 37.7560717855

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Components

#1: Protein alcohol dehydrogenase


Mass: 29525.717 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 % polyethylen glycole 1500, 0.1 M sodium HEPES buffer, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.989→105.434 Å / Num. obs: 43285 / % possible obs: 82.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.56 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.5
Reflection shellResolution: 1.989→2.126 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2163 / CC1/2: 0.644

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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: 1.99→67.13 Å / SU ML: 0.2671 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2404 1082 2.5 %
Rwork0.1991 42172 -
obs0.2001 43254 82.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.89 Å2
Refinement stepCycle: LAST / Resolution: 1.99→67.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 0 448 6145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235790
X-RAY DIFFRACTIONf_angle_d0.52847849
X-RAY DIFFRACTIONf_chiral_restr0.0418940
X-RAY DIFFRACTIONf_plane_restr0.00441030
X-RAY DIFFRACTIONf_dihedral_angle_d13.73962156
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.02241253723
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.20578011252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.3536360.36581377X-RAY DIFFRACTION35.18
2.11-2.190.3774910.27613581X-RAY DIFFRACTION78.78
2.19-2.330.2981540.24196031X-RAY DIFFRACTION95.65
2.33-2.510.26721640.22046356X-RAY DIFFRACTION99.92
2.51-2.760.26071620.2196351X-RAY DIFFRACTION99.98
2.76-3.160.25781650.21196385X-RAY DIFFRACTION99.98
3.16-3.980.23191380.17945384X-RAY DIFFRACTION83.31
3.98-67.130.18891720.16616707X-RAY DIFFRACTION99.49
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)
10.948854180189-0.233894488984-0.006939272811671.5850575871-0.181332854241.02726872424-0.06980204410040.03266966440690.223462071341-0.1963714158490.0706426974519-0.324209746203-0.2803662535410.2864941594670.003143822902220.248595773525-0.07573545595520.004287751425190.298014378047-0.009663420321970.25349844777572.66166865911.1268867909100.350692161
24.87160199632-0.789814561041.029205497192.252060568551.079316775673.962890366980.3467985966280.196769081273-0.84607117468-0.7076079909060.1282701280650.04535374794990.4107115492940.112723301359-0.166769404110.319959471190.0833254257518-0.01261046695770.231709251581-0.08468355865210.33048206425174.6587196725-21.2857822755104.339634277
34.84815087195-0.0453432171144-1.616627759835.9314894052-1.92943974982.09630201665-0.178374872443-0.0868321539281-0.593776413034-0.639236257701-0.0642211260481-0.1906747545620.2028039819730.5085987985660.3192616454830.2265320314770.040655597424-0.03754944950740.2209599056840.01318276255890.49734974511239.607384748813.706910013760.3739074421
42.96086466098-1.17360724504-1.306855396820.687281205433-0.1035809060222.7000779065-0.12361433408-0.0420030492669-0.9064340047940.577654145407-0.165905142887-0.7266656637330.7314961354690.066935652050.2026882969060.478992355176-0.00142223634115-0.08193447460780.2100402638840.0639486182260.61631874841740.53735696258.5301811334466.5898987098
51.190834878210.2477417793290.2254105018612.860726421220.8738665718442.103137037020.03154056142760.0427376885622-0.1580423944350.211746931940.000674764193713-0.4466436703210.1861925780140.0903603111211-0.02429554144620.191955696858-0.00996201672013-0.04302738004880.1920375038410.01552750219790.25996020609839.461128365226.88494189467.2021914362
60.526647320764-0.0843088604726-0.8914870672381.70386403116-1.515444615425.271000593610.0607423883261-0.282586577401-0.22111129622-0.0197625394005-0.3068341798690.3530355004850.346364025180.4118312449520.4535918557060.416979800347-0.1027394119630.03297390368490.4783498242710.02532466798890.27166126921127.011330336617.901055275273.9172602214
71.02418452603-1.45709982645-0.06663256221934.118090891120.6450386334121.255551553030.2029223130540.143137222262-0.409566071272-0.224710966391-0.2793448684940.9781402832570.121722721657-0.360556417790.1004276188910.289971800319-0.0689341608175-0.04277787388420.434971595353-0.07186847246990.33911408570320.375782704726.146712325164.8982941238
84.572956295741.364354495650.9221470639995.549882887030.1975533974685.356459677530.4721497037620.2065496275960.245419832935-0.488815928413-0.6869825875420.666934387284-0.470857110241-0.824462903870.1938457196610.3959154822640.09803614592480.01150051925820.3702231704850.0138486451270.31516542622719.986907057658.766339481468.3875428317
93.35082223710.399318760367-0.08923741183942.79064846087-0.02861891400811.8798398954-0.1681597874670.0778318088170.493757164517-0.1991300773690.1011450963920.056047875079-0.26042913346-0.06393149851750.02897496077290.2993674823580.0218040528617-0.07024256025720.202608104812-0.003087084948940.26707882323242.296702367862.295773957279.2712435821
101.347093092730.4195882013080.3796953595551.902158250831.061155917751.462876535150.0108083943259-0.0268765665078-0.100730452701-0.01301803410670.024164308222-0.26362138493-0.2479950877650.0566787442214-0.04292690879930.254253715947-0.00552019013071-0.03709336209920.2326314554760.01196354294070.23261997390339.558700963245.272841685377.160411711
110.825091389504-0.04810371547460.2404348830980.640055324518-1.102778871456.01340764836-0.01197390878590.2286957712370.171219177576-0.305174591712-0.3100912887670.0155147851118-0.2075099714110.02322574582750.285001152220.4280984852860.0986618521951-0.0431077941650.3651584772720.02990662214860.2500952435929.472458250755.833261871467.0577202781
121.44654761452-0.3312501513350.207353460632.014254287010.9379500703371.198895778390.03964945694940.0376229105488-0.006598330846710.24108203368-0.279998775530.6401709270090.143460190344-0.3743654771090.2416700390040.237264483142-0.01657583293250.04693303402430.391464067396-0.05852898414840.23821893542719.800886326541.353980363573.9260542719
135.200299858871.22306153551-1.467327785234.30868731204-0.03740565274251.752825481040.1363066913380.1936267583870.467641505005-0.4931717002680.06790598907730.00600585288692-0.1539050678480.305258635555-0.2711047730.2906864910890.00894058322418-0.02662301216730.197195579430.01992310685590.27673601261653.469416241922.037914924593.1418228338
143.05963131047-0.6049905518030.8338391831811.599125113130.2544549815923.147303886470.0878834934512-0.09660920606990.514444215298-0.045712365572-0.16992960483-0.0165731142587-0.135506608543-0.1366703872910.08580314839370.2967397901960.00357149414729-0.0291237114290.179689839407-0.02173946488410.27549696480154.204096738524.846611154698.0311536644
152.15855318385-0.268437415272-0.3605683243142.28167881759-0.1741719511331.15455223521-0.03601951237780.05208207944980.16724421733-0.0322108069216-0.07707819951730.374605622315-0.13742343386-0.2012920118230.1253489851560.2844581385170.0285619202642-0.08631651144420.238401738667-0.03464788339310.2992955647146.297115981720.537197601296.3038040862
160.7712747944910.13402281350.1748404564370.9226703335030.004754273509251.49624636038-0.0336261458058-0.001604807345440.04693232146610.0329376277621-0.02420013567070.154459173666-0.198655396722-0.08893697056170.07201549123940.230139228071-0.000586141818996-0.01796103374110.168627038958-0.04238011424990.22389617893356.68043039616.17983801515103.075430816
171.851892647010.8343219587921.855839380981.137674024391.65404962746.23929353437-0.0603509877998-0.3561391124020.136596151727-0.155287480172-0.0066583235846-0.00616592523873-0.474585179202-0.5304150250230.03050985244410.222071142208-0.00267770682413-0.0003210040836460.242584473397-0.0404754585550.24192276494865.459961543218.7124635984110.095177291
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 207 through 248 )CC207 - 248199 - 240
22chain 'C' and (resid 249 through 260 )CC249 - 260241 - 252
33chain 'A' and (resid 2 through 14 )AA2 - 141 - 13
44chain 'A' and (resid 15 through 52 )AA15 - 5214 - 51
55chain 'A' and (resid 53 through 174 )AA53 - 17452 - 173
66chain 'A' and (resid 175 through 206 )AA175 - 206174 - 195
77chain 'A' and (resid 207 through 248 )AA207 - 248196 - 237
88chain 'A' and (resid 249 through 260 )AA249 - 260238 - 249
99chain 'B' and (resid 2 through 52 )BB2 - 521 - 52
1010chain 'B' and (resid 53 through 174 )BB53 - 17453 - 174
1111chain 'B' and (resid 175 through 206 )BB175 - 206175 - 197
1212chain 'B' and (resid 207 through 260 )BB207 - 260198 - 251
1313chain 'C' and (resid 2 through 14 )CC2 - 141 - 13
1414chain 'C' and (resid 15 through 37 )CC15 - 3714 - 36
1515chain 'C' and (resid 38 through 87 )CC38 - 8737 - 86
1616chain 'C' and (resid 88 through 174 )CC88 - 17487 - 174
1717chain 'C' and (resid 175 through 206 )CC175 - 206175 - 198

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