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- PDB-1yw1: Structure Of Ytnj From Bacillus Subtilis in complex with FMN -

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Basic information

Entry
Database: PDB / ID: 1yw1
TitleStructure Of Ytnj From Bacillus Subtilis in complex with FMN
ComponentsPROTEIN YTNJ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NYSGXRC / beta-alpha barrel / FMN / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
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
FLAVIN MONONUCLEOTIDE / alpha-D-glucopyranose / N-acetyl-S-alkylcysteine sulfoxide monooxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsBurley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure Of Ytnj From Bacillus Subtilis in complex with FMN
Authors: Gorman, J. / Shapiro, L.
History
DepositionFeb 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / chem_comp
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN YTNJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3453
Polymers49,7091
Non-polymers6372
Water1,24369
1
A: PROTEIN YTNJ
hetero molecules

A: PROTEIN YTNJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6906
Polymers99,4172
Non-polymers1,2734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area8500 Å2
ΔGint-34 kcal/mol
Surface area30450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.254, 86.254, 194.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second part of the dimeric biological assembly is generated by y-1, x+1, -z

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Components

#1: Protein PROTEIN YTNJ / NITRILOTRIACETATE MONOOXYGENASE COMPONENT A HOMOLOG YTNJ


Mass: 49708.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ytnj / Plasmid: modified pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O34974
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.7 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.5M NACITRATE, 0.1M HEPES PH 7.5, soaked in .01M FMN, CRYO: 30% glucose, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2004
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 17468 / Num. obs: 17468 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.57 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1717 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.182 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.503 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25241 899 5.2 %RANDOM
Rwork0.18221 ---
all0.186 17394 --
obs0.18553 17329 93.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.603 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å20 Å20 Å2
2--2.86 Å20 Å2
3----5.73 Å2
Refinement stepCycle: LAST / Resolution: 2.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 43 69 3207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223213
X-RAY DIFFRACTIONr_bond_other_d00.022856
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9564352
X-RAY DIFFRACTIONr_angle_other_deg0.82936634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4615391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.323.631157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.1615522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2641524
X-RAY DIFFRACTIONr_chiral_restr0.1080.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023589
X-RAY DIFFRACTIONr_gen_planes_other00.02685
X-RAY DIFFRACTIONr_nbd_refined0.2260.2794
X-RAY DIFFRACTIONr_nbd_other0.2160.23048
X-RAY DIFFRACTIONr_nbtor_refined0.1990.21616
X-RAY DIFFRACTIONr_nbtor_other0.1030.21861
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.040.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4651.52231
X-RAY DIFFRACTIONr_mcbond_other0.2591.5802
X-RAY DIFFRACTIONr_mcangle_it2.06623130
X-RAY DIFFRACTIONr_scbond_it3.37831391
X-RAY DIFFRACTIONr_scangle_it5.2614.51222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 62 -
Rwork0.276 1208 -
obs--94.85 %

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