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- PDB-5eow: Crystal Structure of 6-Hydroxynicotinic Acid 3-Monooxygenase from... -

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Basic information

Entry
Database: PDB / ID: 5eow
TitleCrystal Structure of 6-Hydroxynicotinic Acid 3-Monooxygenase from Pseudomonas putida KT2440
Components6-hydroxynicotinate 3-monooxygenase
KeywordsOXIDOREDUCTASE / flavin monooxygenase / oxidative decarboxylase
Function / homology
Function and homology information


6-hydroxynicotinate 3-monooxygenase / 6-hydroxynicotinate 3-monooxygenase activity / nicotinate catabolic process / FAD binding / monooxygenase activity
Similarity search - Function
: / FAD-binding domain / FAD binding domain / 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
FLAVIN-ADENINE DINUCLEOTIDE / 6-hydroxynicotinate 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsYuen, M.E. / Zhen, W. / Gerwig, T.J. / Story, R.W. / Kopp, M. / Nakamoto, K. / Snider, M.J. / Hicks, K.A.
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Biochemical Characterization of 6-Hydroxynicotinic Acid 3-Monooxygenase, A Novel Decarboxylative Hydroxylase Involved in Aerobic Nicotinate Degradation.
Authors: Hicks, K.A. / Yuen, M.E. / Zhen, W.F. / Gerwig, T.J. / Story, R.W. / Kopp, M.C. / Snider, M.J.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 6-hydroxynicotinate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7782
Polymers45,9931
Non-polymers7861
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-4 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.694, 69.469, 115.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 6-hydroxynicotinate 3-monooxygenase / 6HNA monooxygenase / Nicotinate degradation protein C


Mass: 45992.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain KT2440) (bacteria)
Strain: KT2440 / Gene: nicC, PP_3944 / Production host: Escherichia coli (E. coli)
References: UniProt: Q88FY2, 6-hydroxynicotinate 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 41.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris (pH 7.7-8.3), PEG 4000 (27-30%), 0.2 M magnesium chloride hexahydrate
PH range: 7.7-8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Number: 145907 / Rmerge(I) obs: 0.09 / Χ2: 0.38 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 42530 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.75010.0360.3013.6
4.525.710.0410.3233.7
3.954.5210.0390.3223.4
3.593.9510.0470.3533.5
3.333.5910.0590.3823.6
3.143.3310.080.4013.6
2.983.1410.0950.3913.6
2.852.9810.1210.4173.7
2.742.8510.1250.4143.2
2.652.7410.1480.3843.4
2.562.6510.1710.3983.5
2.492.5610.1850.4053.5
2.422.4910.1980.4083.5
2.372.4210.2060.413.5
2.312.3710.2320.4143.5
2.262.3110.240.3993.4
2.222.2610.2560.4043.4
2.182.2210.2660.4013.1
2.142.1810.2920.3942.9
2.12.1410.2990.3953
ReflectionResolution: 2.1→50 Å / Num. obs: 22666 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.05 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.052 / Rrim(I) all: 0.104 / Χ2: 0.385 / Net I/av σ(I): 10.429 / Net I/σ(I): 4.3 / Num. measured all: 145907
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1430.29921010.9020.1870.3550.39597.3
2.14-2.182.90.29221540.8870.1850.3480.39495.6
2.18-2.223.10.26620420.9160.1620.3140.40196.8
2.22-2.263.40.25621720.9360.1490.2980.40498.8
2.26-2.313.40.2421260.9490.1390.2790.39998.7
2.31-2.373.50.23221770.9430.1340.2690.41499
2.37-2.423.50.20621160.9510.1180.2390.4198.7
2.42-2.493.50.19821700.9520.1130.2290.40898.2
2.49-2.563.50.18521350.9680.1060.2140.40598.4
2.56-2.653.50.17121200.9670.0970.1980.39898.1
2.65-2.743.40.14821240.9740.0860.1720.38497.9
2.74-2.853.20.12520750.9750.0740.1460.41495.2
2.85-2.983.70.12121770.9850.0670.1390.41799
2.98-3.143.60.09521440.9890.0530.1090.39199.2
3.14-3.333.60.0821560.9940.0440.0920.40198.9
3.33-3.593.60.05921270.9960.0330.0680.38298
3.59-3.953.50.04721030.9970.0270.0550.35397.1
3.95-4.523.40.03920730.9980.0220.0450.32295.4
4.52-5.73.70.04121440.9980.0220.0470.32398.1
5.7-503.60.03620940.9990.0190.0410.30195.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
AutoSolphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.393 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1966 8.67 %
Rwork0.2061 20698 -
obs0.2101 22664 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.88 Å2 / Biso mean: 17.7826 Å2 / Biso min: 5.37 Å2
Refinement stepCycle: final / Resolution: 2.1→44.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 53 52 2828
Biso mean--13.59 14.34 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082846
X-RAY DIFFRACTIONf_angle_d0.8633869
X-RAY DIFFRACTIONf_chiral_restr0.05415
X-RAY DIFFRACTIONf_plane_restr0.006494
X-RAY DIFFRACTIONf_dihedral_angle_d12.2541635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14810.26331380.20161440157897
2.1481-2.20620.28191370.22471439157697
2.2062-2.27110.30531430.21151492163599
2.2711-2.34440.3041350.20981446158198
2.3444-2.42820.2861400.21371464160499
2.4282-2.52540.2441390.21421468160798
2.5254-2.64040.25171350.22321463159897
2.6404-2.77950.26151390.22581466160598
2.7795-2.95370.28041410.22851471161298
2.9537-3.18160.29071440.23011519166399
3.1816-3.50170.27991420.21281480162298
3.5017-4.00810.22291400.1871473161396
4.0081-5.04870.19351430.16551498164197
5.0487-44.40280.22561500.20311579172996

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