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- PDB-7pcs: Structure of the heterotetrameric SDR family member BbsCD -

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Basic information

Entry
Database: PDB / ID: 7pcs
TitleStructure of the heterotetrameric SDR family member BbsCD
Components
  • BbsC
  • BbsD
KeywordsOXIDOREDUCTASE / SDR family / pseudoenzyme / heterotetramer / anaerobic toluene degradation / enzyme / dehydrogenase
Function / homologyShort-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / BbsD / BbsC
Function and homology information
Biological speciesThauera aromatica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsEssen, L.-O. / Heider, J. / von Horsten, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB987 Germany
CitationJournal: Febs J. / Year: 2022
Title: Inactive pseudoenzyme subunits in heterotetrameric BbsCD, a novel short-chain alcohol dehydrogenase involved in anaerobic toluene degradation.
Authors: von Horsten, S. / Lippert, M.L. / Geisselbrecht, Y. / Schuhle, K. / Schall, I. / Essen, L.O. / Heider, J.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BbsC
B: BbsD
C: BbsC
D: BbsD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,08314
Polymers103,0194
Non-polymers2,06410
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.600, 68.600, 191.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 25 or resid 27...
d_2ens_1(chain "C" and (resid 7 through 25 or resid 27...
d_1ens_2(chain "B" and (resid 2 through 196 or (resid 197...
d_2ens_2(chain "D" and (resid 2 through 195 or (resid 196...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYLEUA1 - 19
d_12ens_1LEULEUA21 - 138
d_13ens_1TYRLYSA140 - 202
d_14ens_1LEUILEA204 - 244
d_21ens_1GLYLEUC1 - 19
d_22ens_1LEULEUC21 - 138
d_23ens_1TYRLYSC140 - 202
d_24ens_1LEUILEC204 - 244
d_11ens_2GLYVALB1 - 238
d_12ens_2GLYGLYB240 - 241
d_13ens_2SERGLYB243 - 247
d_21ens_2GLYVALD1 - 238
d_22ens_2GLYGLYD240 - 241
d_23ens_2SERGLYD243 - 247

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.781841730842, -0.622808271108, -0.0288680680742), (-0.622778948202, -0.782319174085, 0.0110946624807), (-0.0294938907313, 0.00930415495484, -0.999521657149)-4.09498344491, -14.7238246861, 60.4532505971
2given(0.780328956579, -0.624875622735, -0.0248430198554), (-0.624638996657, -0.780721730455, 0.0173119453066), (-0.0302132980554, 0.00200890677898, -0.999541455325)-4.13657712504, -14.7520779035, 60.6124212979

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Components

#1: Protein BbsC


Mass: 25310.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pseudoenzyme subunit BbsC / Source: (gene. exp.) Thauera aromatica (bacteria) / Gene: bbsC / Plasmid: pTrc99A / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q9KJF2
#2: Protein BbsD


Mass: 26198.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Enzymatic subunits of BbsCD heterotetramer / Source: (gene. exp.) Thauera aromatica (bacteria) / Gene: bbsD / Plasmid: pTrc99A / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q9KJF1
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35 mg/ml BbsCD, 2mM NAD+, 2mM benzylsuccinyl-CoA, 0.2 M Mg(CH3COO)2, 0.1 M sodium cacodylate, pH 6.5 and 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.894 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2013
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.894 Å / Relative weight: 1
ReflectionResolution: 2.25→43.54 Å / Num. obs: 46066 / % possible obs: 96.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Net I/σ(I): 19.5
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 6818 / CC1/2: 0.858 / Rpim(I) all: 0.247 / Rrim(I) all: 0.461 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→29.7 Å / SU ML: 0.2064 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.5641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 961 2.09 %
Rwork0.1842 45091 -
obs0.1847 46052 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.62 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 136 297 7533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00587393
X-RAY DIFFRACTIONf_angle_d0.772310032
X-RAY DIFFRACTIONf_chiral_restr0.04771180
X-RAY DIFFRACTIONf_plane_restr0.00711307
X-RAY DIFFRACTIONf_dihedral_angle_d14.71282656
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.621576630846
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.720654086911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.27581520.26256552X-RAY DIFFRACTION97.3
2.37-2.520.28281560.23736499X-RAY DIFFRACTION97.7
2.52-2.710.2181960.21836553X-RAY DIFFRACTION97.31
2.71-2.990.25931500.21556488X-RAY DIFFRACTION96.83
2.99-3.420.24561410.20396407X-RAY DIFFRACTION96.01
3.42-4.30.18441370.15886330X-RAY DIFFRACTION94.98
4.3-29.70.1621290.1496262X-RAY DIFFRACTION93.44
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)
10.766169122474-0.2036232165380.001077103657840.142197134882-0.0221655861780.0257387594663-0.1015602071280.0927631596609-0.0154991802678-0.07315517252340.0152529945969-0.2775968987610.01851892555960.145359747969-0.08566228742460.202556393933-0.1387308307340.09388047959151.01166478296-0.04720049533010.56565040574527.178600906-4.221089969677.80234615756
21.890818649870.146023641301-0.3381116187470.531628656494-0.1067373187111.29869867694-0.2163818122050.154198493925-0.177802891609-0.03508720104130.122031121163-0.1774430241350.1904740687560.4552944156520.08426729696540.189997386112-0.001440022784780.04189843451330.766538643009-0.06071698053270.43986036569314.8614541962-9.9812408042519.1510300038
33.853655089470.917406133732-0.4862705330262.67771100583-0.4866129138033.36195858873-0.0286880863941-0.08879720185070.2589020719070.247043956470.2503979717380.079764411996-0.51209272421-0.141177349013-0.1893934222980.3397740142530.01697960437030.006788592170770.4745781283360.01489752723150.252428108894-6.5132703427712.151637959510.9960656326
41.561935900771.08670631855-1.654110846091.29159861241-0.6560456266192.297685354110.0638428349267-0.1953365228680.1449960631210.03977997836470.1652775989520.386340957963-0.56197889598-0.497066795709-0.1695994180130.4518198986390.264194705335-0.0006107810951250.7897428150830.1055875982250.451203956421-16.011288091514.041618380210.3982724404
50.840946551324-0.134649125571-0.6066456741670.739737361638-0.5606519315346.24301293193-0.2138073529140.127555708673-0.02697441677590.1508406336880.1196280474770.0318631414671-0.399880385373-0.2531103000590.09586419546290.2966713196420.135572477050.005830656963260.649212195560.009860405046590.34246344753-11.93594921996.4824211272326.6467604105
61.26469766183-0.109744431767-0.1800371871950.769657953515-0.3400965422840.192403095538-0.1891348034920.072573710281-0.07433528583090.0599500078340.2217414187960.0818921726476-0.12607786518-0.37069095574-0.01451645998240.1743057010020.0843690839529-0.003576182624840.7108605885010.01598364611430.370770391507-10.9427761009-1.2577220691822.3198646796
73.137952749860.0029158155831-0.02172538470971.05777254847-1.326030069682.74656932528-0.072302376031-0.7583887344040.7971848385940.593734658042-0.2349638781340.248690958922-0.861761390905-0.3513879267260.338345218030.4815704451090.122659818657-0.007417571578060.714282425462-0.1887938714070.541951720544-1.0760525560311.613161145525.0052559914
82.487566091710.0882615768961-0.2024310222541.031972024151.823426770393.273472996820.0243159294961-1.169836240790.6784327310931.145892700310.1604250660950.12658755582-0.737641499136-0.0959693587092-0.1988270414340.99300209961-0.07121706403860.006274330166161.01648685475-0.3458824609280.7035983783937.9386113898915.600204516834.2507617343
91.24441499934-0.1674106402620.9687303506531.0427171721-1.023374141661.53710604672-0.1737722308270.00418336689119-0.06498519700910.127505982650.034331697319-0.0501254993258-0.327265814629-0.08770244760090.1270974680090.18571122873-0.00562975736285-0.001746612657420.496186478264-0.0326194834630.3174158756823.892539687832.432423439519.4290001038
100.826315886415-0.441245101830.1239687027260.377893834059-0.09167427144470.0232130487652-0.006950070784140.111591239959-0.131488142104-0.0799736168587-0.10575975845-0.2287089879390.1454704211780.179560203076-0.2257227056020.7502856304030.5430373836480.03434774135130.7884560275620.08866022743650.55754206011519.5391139139-28.304405253651.8094372458
111.53865713438-0.631663919096-0.4584520359230.7507045334370.108399646150.898094706919-0.247557596598-0.004777833126620.009105305968190.290326779760.200533303786-0.2531404893960.3377518891830.5971101613750.03621766432640.3769936228790.245972478713-0.02323925761950.678821201457-0.03164965337040.37085535880913.2035218564-15.9500004140.7840633677
121.92763686974-0.2294999486720.6334834407591.50517591655-0.2514634132182.015456341-0.0294630131518-0.000382181475896-0.1438665219020.1599950203540.1929121620240.2286807371790.193808545439-0.481412897958-0.1277385719490.4205972943540.05864672333430.10922107270.706920941230.09875808320440.394914517499-17.2646780485-19.921900380549.8626017977
130.141333296260.05660348601-0.5268590657470.6553679600450.2077019634282.2414330623-0.182082958311-0.223072987177-0.2191314408790.273801243381-0.05083942055460.3352822579040.341086086292-0.4944685784750.2704302656490.4294088882140.09146757634350.2300458068991.078373560840.1863375871680.651971354425-25.667568464-15.461290359950.9040279994
140.436720922979-0.4651319721610.2221505624280.849071399286-0.354580730940.152103449946-0.2887051421790.0386170926949-0.04809792256180.1237338909890.2988530839590.189867007351-0.0536580571251-0.3689517146020.01702336732510.261408186085-0.001998872567110.08782037253560.8548609968190.06624076140590.461780734948-18.3102011537-11.835565299534.4287359113
150.842316375162-0.1721753988260.4596576625321.088994384570.0377168661460.268504064431-0.1921915241090.119672774075-0.03569702619590.1479780180850.2248733929810.0960368893606-0.0172448479046-0.364664382759-0.0126564603420.1928926762760.1201145851970.05383159820030.6911955330490.05707874709720.380945813428-12.4528278157-6.4722708356138.7086985913
160.782460414781-1.39763696505-1.180154250353.082984038671.00878465183.83429364422-0.1006423567320.22899350833-0.29143965466-0.371240883878-0.2882311305380.7882614490710.50271073174-0.8839503434370.3406495696160.374967075908-0.02076137332-0.006285640235950.734065506454-0.0632587395870.499952664077-12.648183109-22.803358296535.1018865415
171.135004604250.198508987051.34090875832.062679783781.255629277662.10919596544-0.02317910803440.380777864148-0.229171854545-0.4232674520330.06662016159930.2906495379780.355539703195-0.232051520733-0.05078972678040.867024528088-0.1991151964490.08547467305270.87742676432-0.06161289969540.758020452301-7.8890423938-32.256139807226.4540284941
181.383320821250.0873406980539-1.00413184441.21550625611-0.4897194916772.25331950627-0.3004272765610.0603889408381-0.1857510803510.02450983360250.153564039-0.06113084875340.43609055999-0.2526517862870.1335633042020.338041320220.1038456611730.05160182562380.5424313610990.01656220737750.342128024527-3.18144583418-18.916229558740.6842958559
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 82 )AA7 - 821 - 76
22chain 'A' and (resid 83 through 250 )AA83 - 25077 - 244
33chain 'B' and (resid 2 through 38 )BB2 - 381 - 37
44chain 'B' and (resid 39 through 80 )BB39 - 8038 - 79
55chain 'B' and (resid 81 through 102 )BB81 - 10280 - 101
66chain 'B' and (resid 103 through 174 )BB103 - 174102 - 173
77chain 'B' and (resid 175 through 195 )BB175 - 195174 - 194
88chain 'B' and (resid 196 through 213 )BB196 - 213195 - 212
99chain 'B' and (resid 214 through 248 )BB214 - 248213 - 247
1010chain 'C' and (resid 7 through 82 )CC7 - 821 - 76
1111chain 'C' and (resid 83 through 250 )CC83 - 25077 - 244
1212chain 'D' and (resid 2 through 38 )DD2 - 381 - 37
1313chain 'D' and (resid 39 through 80 )DD39 - 8038 - 79
1414chain 'D' and (resid 81 through 102 )DD81 - 10280 - 101
1515chain 'D' and (resid 103 through 174 )DD103 - 174102 - 173
1616chain 'D' and (resid 175 through 195 )DD175 - 195174 - 194
1717chain 'D' and (resid 196 through 213 )DD196 - 213195 - 212
1818chain 'D' and (resid 214 through 248 )DD214 - 248213 - 247

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