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- PDB-1tvl: Structure of YTNJ from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1tvl
TitleStructure of YTNJ from Bacillus subtilis
Componentsprotein YTNJ
KeywordsOXIDOREDUCTASE / beta-alpha barrel / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-acetyl-S-alkylcysteine sulfoxide monooxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.104 Å
AuthorsGorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of YTNJ from Bacillus subtilis
Authors: Gorman, J. / Shapiro, L.
History
DepositionJun 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: protein YTNJ


Theoretical massNumber of molelcules
Total (without water)50,8341
Polymers50,8341
Non-polymers00
Water4,161231
1
A: protein YTNJ

A: protein YTNJ


Theoretical massNumber of molelcules
Total (without water)101,6672
Polymers101,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area5940 Å2
ΔGint-19 kcal/mol
Surface area30560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.941, 85.941, 196.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein protein YTNJ / E.C.1.14.13.- / nitrilotriacetate monooxygenase component A homolog ytnJ


Mass: 50833.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YTNJ / Plasmid: Modified PET26B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O34974, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5M NaCitrate, 0.1M Hepes pH 7.5, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2003
RadiationMonochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.104→20 Å / Num. all: 43243 / Num. obs: 43146 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 16.4
Reflection shellResolution: 2.104→2.17 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.104→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.335 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.139 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22801 2179 5.1 %RANDOM
Rwork0.20668 ---
all0.20775 43146 --
obs0.20775 43146 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.766 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2--2.09 Å20 Å2
3----4.19 Å2
Refinement stepCycle: LAST / Resolution: 2.104→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 0 231 3299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223140
X-RAY DIFFRACTIONr_bond_other_d0.0010.022802
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9234246
X-RAY DIFFRACTIONr_angle_other_deg0.79436515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13423.782156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84315518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9551523
X-RAY DIFFRACTIONr_chiral_restr0.0740.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
X-RAY DIFFRACTIONr_nbd_refined0.2070.2665
X-RAY DIFFRACTIONr_nbd_other0.1880.22871
X-RAY DIFFRACTIONr_nbtor_other0.0870.21690
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.215
X-RAY DIFFRACTIONr_mcbond_it0.9881.52492
X-RAY DIFFRACTIONr_mcbond_other0.1391.5796
X-RAY DIFFRACTIONr_mcangle_it1.12823106
X-RAY DIFFRACTIONr_scbond_it1.95131390
X-RAY DIFFRACTIONr_scangle_it2.7624.51140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
2.104-2.2160.2453060.2165834X-RAY DIFFRACTION9
2.216-2.3490.2322890.209X-RAY DIFFRACTION9
2.349-2.5090.2432810.208X-RAY DIFFRACTION9
2.509-2.7060.2432470.208X-RAY DIFFRACTION9
2.706-2.9590.2412610.217X-RAY DIFFRACTION9
2.959-3.2990.2292120.201X-RAY DIFFRACTION9
3.299-3.7920.2181860.188X-RAY DIFFRACTION9
4.603-6.3440.2361420.207X-RAY DIFFRACTION9
6.344-200.264800.261X-RAY DIFFRACTION9

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