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- PDB-6y8j: Crystal structure of the apo form of a quaternary ammonium Rieske... -

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Basic information

Entry
Database: PDB / ID: 6y8j
TitleCrystal structure of the apo form of a quaternary ammonium Rieske monooxygenase CntA
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] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Carnitine monooxygenase oxygenase subunit
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)44,9562
Polymers44,7801
Non-polymers1761
Water1,18966
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)134,8686
Polymers134,3413
Non-polymers5273
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area8270 Å2
ΔGint-81 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.600, 91.600, 82.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#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
Plasmid: pET-28 a (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A059ZPP5, carnitine monooxygenase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.18 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: 1.7397 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: 1.7397 Å / Relative weight: 1
ReflectionResolution: 2.05→45.8 Å / Num. obs: 24733 / % possible obs: 99.3 % / Redundancy: 9.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.066 / Rrim(I) all: 0.206 / Net I/σ(I): 7.4 / Num. measured all: 225029 / Scaling rejects: 544
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.15.31.452960218060.4080.6781.6071.199.3
9.17-45.8100.10229262930.9930.0340.10818.598.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
DIALS0.7.3data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VCP

3vcp


Resolution: 2.05→40 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.94
RfactorNum. reflection% reflection
Rfree0.2482 1223 4.95 %
Rwork0.2014 --
obs0.2036 24704 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.09 Å2 / Biso mean: 55.7937 Å2 / Biso min: 23.94 Å2
Refinement stepCycle: final / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 4 66 2865
Biso mean--44.74 44.42 -
Num. residues----343
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0501-2.13220.51141130.4208261899
2.1322-2.22920.42851560.3494258299
2.2292-2.34680.33721400.2934257799
2.3468-2.49380.33461330.2658256799
2.4938-2.68630.26681400.2296261199
2.6863-2.95650.26711360.1959260199
2.9565-3.38420.20481320.17752617100
3.3842-4.26290.24651560.16522614100
4.2629-400.16411170.15982694100
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)
14.32170.2094-1.10922.84720.0462.2225-0.0113-0.3786-0.23570.27640.0660.0810.0859-0.2741-0.01070.24120.0152-0.08350.31030.03650.4039-32.06838.9172-1.2759
22.12-0.70950.40526.41970.82151.96220.00820.29270.8001-0.27180.1706-0.4531-0.2403-0.0014-0.17230.2883-0.01980.0410.3130.06140.6406-15.034826.0429-11.5771
31.25161.15780.29753.16392.27131.9208-0.4708-0.7241.43320.27430.4604-0.4386-0.62040.5071-0.16310.532-0.0485-0.15810.5499-0.08131.3872-8.766933.9564-3.479
43.5154-0.22930.21155.63130.33173.0459-0.1017-0.0946-0.85490.2723-0.0037-0.46150.14540.28990.07670.20160.022-0.00630.29870.04650.473-17.61082.3393-6.3236
50.6618-0.2257-1.17971.1992-0.51562.3222-0.37450.107-1.3024-0.24230.020.02530.435-0.43150.32920.3521-0.07150.04150.4376-0.02390.8622-37.24280.7912-12.9957
62.49280.686-1.36265.03450.91233.5379-0.40850.0444-1.2978-0.2230.01710.66430.56520.03950.24560.34210.00310.0320.2835-0.0570.843-28.6596-3.6564-10.4055
73.4508-2.4738-0.78476.78385.09854.23380.0999-0.00370.2994-0.41090.3662-0.1584-0.30150.3699-0.41660.3517-0.01030.00440.3437-0.0060.6006-28.07026.2971-20.5905
84.8899-1.8372-7.29541.0342.17388.6159-0.19831.1201-1.0333-0.1445-0.29980.1670.0839-0.98960.5720.3084-0.0362-0.0040.6382-0.19460.7351-39.77783.8117-20.8986
93.7732-2.38870.96992.3333-1.92262.526-0.0809-0.697-1.7184-0.0261-0.0720.28120.16340.13210.27940.3543-0.0040.02840.53660.2361.0435-42.3432-3.58571.2717
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 182 )A142 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 225 )A183 - 225
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 287 )A226 - 287
7X-RAY DIFFRACTION7chain 'A' and (resid 288 through 305 )A288 - 305
8X-RAY DIFFRACTION8chain 'A' and (resid 306 through 335 )A306 - 335
9X-RAY DIFFRACTION9chain 'A' and (resid 336 through 371 )A336 - 371

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