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- PDB-6y8s: Crystal structure of the quaternary ammonium Rieske monooxygenase... -

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Basic information

Entry
Database: PDB / ID: 6y8s
TitleCrystal structure of the quaternary ammonium Rieske monooxygenase CntA in complex with substrate gamma-butyrobetaine
ComponentsCarnitine monooxygenase oxygenase subunit
KeywordsOXIDOREDUCTASE / Apo / Rieske / Iron-Sulphur Cluster
Function / homology
Function and homology information


carnitine monooxygenase / carnitine metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Carnitine monooxygenase oxygenase subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / 3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM / Carnitine monooxygenase oxygenase subunit
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.629 Å
AuthorsQuareshy, M. / Shanmugam, M. / Bugg, T.D. / Cameron, A. / Chen, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2016-307 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer.
Authors: Quareshy, M. / Shanmugam, M. / Townsend, E. / Jameson, E. / Bugg, T.D.H. / Cameron, A.D. / Chen, Y.
History
DepositionMar 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3966
Polymers44,7801
Non-polymers6165
Water4,288238
1
A: Carnitine monooxygenase oxygenase subunit
hetero molecules

A: Carnitine monooxygenase oxygenase subunit
hetero molecules

A: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,18918
Polymers134,3413
Non-polymers1,84915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9920 Å2
ΔGint-129 kcal/mol
Surface area40310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.160, 91.160, 81.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carnitine monooxygenase oxygenase subunit / Carnitine monooxygenase alpha subunit


Mass: 44780.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, ...Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, DOL94_04925, DVA79_16365, E2533_13315, E2536_16135, E5294_15630, E5979_13670, EA685_07170, EA686_01565, EA706_03020, EA722_03860, EA746_003300, EWO92_12480, EWO96_16565, EWP49_15025, FD887_09300, FD913_14110, FJU36_15000, FJU42_16200, FJU76_14830, FJU79_08840, FJU87_10695, FJV14_20515, LV38_02893, NCTC13305_01609, SAMEA104305283_02985, SAMEA104305351_01970
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A059ZPP5, carnitine monooxygenase

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Non-polymers , 5 types, 243 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NM2 / 3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM


Mass: 146.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.64 % / Description: Red Hexagonal Crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 10mM HEPES, 20% PEG3350, 0.2M NaSCN, 0.5mM TCEP / PH range: 7.0 - 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.3 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.629→39.778 Å / Num. obs: 47464 / % possible obs: 94.37 % / Redundancy: 4.3 % / Biso Wilson estimate: 23.88 Å2 / CC1/2: 0.982 / CC star: 0.996 / Rmerge(I) obs: 0.1341 / Rpim(I) all: 0.06975 / Rrim(I) all: 0.1517 / Net I/σ(I): 6.79
Reflection shellResolution: 1.629→1.687 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.7547 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 4434 / CC1/2: 0.517 / CC star: 0.825 / Rpim(I) all: 0.5946 / Rrim(I) all: 0.9674 / % possible all: 93.43

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VCP

3vcp


Resolution: 1.629→39.778 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.1928 4480 5.01 %
Rwork0.1703 --
obs0.1714 47464 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.41 Å2 / Biso mean: 35.5658 Å2 / Biso min: 15.42 Å2
Refinement stepCycle: final / Resolution: 1.629→39.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 31 238 3101
Biso mean--49.64 41.22 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6292-1.64770.36621240.3387224676
1.6477-1.66710.37261220.3326243280
1.6671-1.68740.29481360.3071244583
1.6874-1.70870.32281340.2963258285
1.7087-1.73120.28961400.2786261888
1.7312-1.75490.27851510.2572276691
1.7549-1.780.26871410.2551271391
1.78-1.80660.23391370.2353276692
1.8066-1.83480.22871520.2153281793
1.8348-1.86490.24771450.2051280494
1.8649-1.89710.2151440.1989281994
1.8971-1.93160.20231480.1886290196
1.9316-1.96870.22861120.18295697
1.9687-2.00890.18651450.1758296399
2.0089-2.05260.2041480.1718298599
2.0526-2.10030.21462070.1675290599
2.1003-2.15280.23541590.1682295699
2.1528-2.2110.19581210.1684300999
2.211-2.27610.2111770.1648298899
2.2761-2.34950.211820.1691292299
2.3495-2.43350.17971870.1641286598
2.4335-2.53090.18651470.1708296898
2.5309-2.64610.16191250.1716297698
2.6461-2.78560.22731820.1725289198
2.7856-2.960.19931460.1651297298
2.96-3.18850.15381610.1564290098
3.1885-3.50920.16921550.1579295297
3.5092-4.01660.1871130.1404296098
4.0166-5.05880.14661900.1367287897
5.0588-39.80.19571490.1741289997
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)
11.3413-0.45650.04832.3481-0.09240.32510.10220.2586-0.1298-0.278-0.07350.1110.15670.035800.22780.0368-0.01310.24570.00640.127823.6765-23.19471.1424
21.93440.3939-0.41221.0662-0.34150.60450.0384-0.18820.45980.16220.0786-0.1366-0.06850.14490.00070.19760.0103-0.00930.209-0.01920.235329.88010.025611.4155
31.0524-0.1957-0.35230.54990.20120.316-0.01170.4861.0702-0.4247-0.0196-0.2616-0.27740.2175-0.0150.3304-0.01640.02850.35320.14570.60733.56829.27383.2435
40.8909-0.04960.62410.84470.1080.45270.0940.31090.2671-0.1431-0.02430.274-0.1207-0.08140.00040.20090.0221-0.02230.24570.03920.191814.4725-11.85062.0436
51.1460.11360.31551.15370.11051.58220.0015-0.0544-0.10380.06760.00380.24040.0334-0.0508-0.00140.17050.00930.01790.15590.02560.193115.7079-22.896212.9533
62.14970.2146-0.58261.85241.58691.47050.0683-0.2516-1.05970.6654-0.27370.46610.6666-0.0146-0.00310.4296-0.04090.02040.33860.0050.62498.9095-34.9679.3133
71.1872-0.34221.33971.47730.29651.7702-0.0444-0.4298-0.27630.3394-0.01220.41280.3087-0.19630.00270.2428-0.00290.0650.24250.03010.29568.5532-26.68112.9438
81.41640.4880.27040.9508-0.85541.2059-0.1135-0.0369-0.10110.25350.09360.0760.1537-0.07050.00040.21140.00910.03720.16210.02310.156219.8376-21.570317.4161
90.1233-0.6849-0.7577-0.09520.95860.4097-0.1051-0.0675-0.16140.30210.11150.16230.2751-0.0410.00050.44450.08560.06490.31050.02720.27422.9644-32.402220.6297
100.8877-0.80740.51571.7012-0.01210.92640.11650.1461-0.5182-0.3076-0.15480.6780.1003-0.2061-0.01360.3680.0536-0.11140.3069-0.05530.386118.1616-38.3105-1.449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 66 )A4 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 114 )A67 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 141 )A115 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 167 )A142 - 167
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 203 )A168 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 239 )A204 - 239
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 276 )A240 - 276
8X-RAY DIFFRACTION8chain 'A' and (resid 277 through 305 )A277 - 305
9X-RAY DIFFRACTION9chain 'A' and (resid 306 through 335 )A306 - 335
10X-RAY DIFFRACTION10chain 'A' and (resid 336 through 371 )A336 - 371

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