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- PDB-6cr0: 1.55 A resolution structure of (S)-6-hydroxynicotine oxidase from... -

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Basic information

Entry
Database: PDB / ID: 6cr0
Title1.55 A resolution structure of (S)-6-hydroxynicotine oxidase from Shinella HZN7
Components(S)-6-hydroxynicotine oxidase
KeywordsOXIDOREDUCTASE / amine oxidase / FAD binding
Function / homology
Function and homology information


(S)-6-hydroxynicotine oxidase / (S)-6-hydroxynicotine oxidase activity / nicotine catabolic process / alkaloid metabolic process / nucleotide binding
Similarity search - Function
: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / (S)-6-hydroxynicotine oxidase
Similarity search - Component
Biological speciesShinella sp. HZN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.548 Å
AuthorsDeay III, D. / Lovell, S. / Battaile, K.P. / Petillo, P. / Richter, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)2R44DA033701 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2022
Title: Improving the kinetic parameters of nicotine oxidizing enzymes by homologous structure comparison and rational design
Authors: Deay, D.O. / Seibold, S. / Battaile, K.P. / Lovell, S. / Richter, M.L. / Petillo, P.A.
History
DepositionMar 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 26, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (S)-6-hydroxynicotine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3438
Polymers49,0641
Non-polymers1,2797
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein is a functional monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.282, 96.282, 78.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-858-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein (S)-6-hydroxynicotine oxidase


Mass: 49064.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shinella sp. HZN7 (bacteria) / Gene: nctB, shn_30305 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A075BSX9, (S)-6-hydroxynicotine oxidase

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.14 Å3/Da / Density % sol: 42.64 % / Description: Prism
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.05 M calcium acetate, 0.1 M sodium cacodylate, 25 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.548→48.14 Å / Num. obs: 61448 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 22.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.55-1.5791.34929450.663197.2
8.48-48.148.80.0564310.995199.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXdev_3080refinement
XDSdata reduction
Aimless0.5.15data scaling
PDB_EXTRACT3.24data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD
Starting model: crank2 SAD solution

Resolution: 1.548→31.516 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 17.84
Details: The structure was solved by SAD phasing using Pt soaked crystals. The resulting initial model was used for molecular replacement against the native which produced the final structure.
RfactorNum. reflection% reflection
Rfree0.1851 3082 5.02 %
Rwork0.1488 --
obs0.1505 61404 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.27 Å2 / Biso mean: 30.3184 Å2 / Biso min: 13.27 Å2
Refinement stepCycle: final / Resolution: 1.548→31.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 83 276 3682
Biso mean--30.24 35.8 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5483-1.57250.23461200.23972586270697
1.5725-1.59830.2731350.227825952730100
1.5983-1.62580.26041660.216525942760100
1.6258-1.65540.23421320.204226332765100
1.6554-1.68720.21061510.192426592810100
1.6872-1.72170.24591280.19226262754100
1.7217-1.75910.20171470.187525992746100
1.7591-1.80.20751040.180426772781100
1.8-1.8450.19981540.179525992753100
1.845-1.89490.19361410.165726682809100
1.8949-1.95070.23071600.168125922752100
1.9507-2.01360.17321470.154226292776100
2.0136-2.08560.18521500.155226352785100
2.0856-2.1690.18871430.146526792822100
2.169-2.26770.17321360.14126382774100
2.2677-2.38730.16341380.137726502788100
2.3873-2.53680.18511870.140826432830100
2.5368-2.73250.21631120.143426592771100
2.7325-3.00730.18971450.142226972842100
3.0073-3.4420.17081340.139527122846100
3.442-4.33480.13591380.123427012839100
4.3348-31.52220.20291140.148228512965100
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)
10.17060.0842-0.07460.0357-0.01110.18970.0099-0.0251-0.06330.021-0.20920.21830.1135-0.2185-0.22020.16490.0305-0.0140.2894-0.13720.299976.875175.362393.6781
20.09110.1040.0980.11620.12750.1271-0.0071-0.0067-0.0091-0.1625-0.0155-0.1107-0.20840.0684-0.00930.23820.01090.03330.15640.02190.1865101.476183.778589.4066
30.06510.0217-0.05210.1593-0.14430.2101-0.04350.03340.0333-0.1096-0.23550.2687-0.0911-0.3442-0.77250.2690.1537-0.16260.4439-0.22170.415269.323183.566885.7362
40.338-0.0664-0.09660.228-0.07420.0701-0.0430.00730.0369-0.0731-0.07910.0366-0.1896-0.1993-0.1480.37170.1201-0.09440.202-0.02890.182385.15882.361778.5394
50.0136-0.0256-0.01270.05470.05660.05820.05020.0282-0.0131-0.0937-0.0704-0.04550.0015-0.0095-00.23890.0150.01220.15850.00390.17394.577764.113580.7362
60.00460.00080.00810.00820.01040.022-0.01720.0297-0.0115-0.0963-0.1149-0.0267-0.0607-0.0203-00.2310.0422-0.01560.2116-0.03990.193391.892562.30874.6667
70.0115-0.00430.00710.0079-0.00620.00470.0150.0763-0.0452-0.1062-0.07280.0713-0.1623-0.1345-00.37240.0899-0.06870.2256-0.03120.232684.584588.979481.8525
80.11090.0995-0.11640.1402-0.13970.1457-0.0371-0.05860.0587-0.1358-0.19060.2062-0.1653-0.2593-0.32360.24270.1281-0.09780.2937-0.14060.295475.773991.490192.9205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 88 )A5 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 200 )A89 - 200
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 275 )A201 - 275
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 297 )A276 - 297
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 344 )A298 - 344
6X-RAY DIFFRACTION6chain 'A' and (resid 345 through 371 )A345 - 371
7X-RAY DIFFRACTION7chain 'A' and (resid 372 through 394 )A372 - 394
8X-RAY DIFFRACTION8chain 'A' and (resid 395 through 434 )A395 - 434

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