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- PDB-1tuv: Crystal structure of YgiN in complex with menadione -

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Basic information

Entry
Database: PDB / ID: 1tuv
TitleCrystal structure of YgiN in complex with menadione
ComponentsProtein ygiN
KeywordsUNKNOWN FUNCTION / menadione oxidase / monooxygenase / co-crystal with natural product / ferredoxin fold
Function / homology
Function and homology information


Oxidoreductases / response to acidic pH / catalytic activity / oxidoreductase activity / protein homodimerization activity / cytosol
Similarity search - Function
: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MENADIONE / Probable quinol monooxygenase YgiN / Probable quinol monooxygenase YgiN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / direct input of native model / Resolution: 1.7 Å
AuthorsAdams, M.A. / Jia, Z.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and Biochemical Evidence for an Enzymatic Quinone Redox Cycle in Escherichia coli: IDENTIFICATION OF A NOVEL QUINOL MONOOXYGENASE
Authors: Adams, M.A. / Jia, Z.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ygiN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9482
Polymers12,7761
Non-polymers1721
Water3,261181
1
A: Protein ygiN
hetero molecules

A: Protein ygiN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8964
Polymers25,5512
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
2
A: Protein ygiN
hetero molecules

A: Protein ygiN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8964
Polymers25,5512
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area3800 Å2
ΔGint-32 kcal/mol
Surface area10270 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.562, 102.562, 102.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-4610-

HOH

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Components

#1: Protein Protein ygiN


Mass: 12775.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygiN / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40718, UniProt: P0ADU2*PLUS
#2: Chemical ChemComp-VK3 / MENADIONE / VITAMIN K3 / 2-METHYL-1,4-NAPHTHALENEDIONE


Mass: 172.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.24 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, ammonium sulfate, sodium/potassium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2004
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. all: 19783 / Num. obs: 19783 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 50
Reflection shellResolution: 1.69→1.77 Å / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: direct input of native model / Resolution: 1.7→25.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.913 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24904 1056 5.1 %RANDOM
Rwork0.20756 ---
all0.20949 19783 --
obs0.20949 19783 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.765 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 0 13 181 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021829
X-RAY DIFFRACTIONr_bond_other_d0.0030.02756
X-RAY DIFFRACTIONr_angle_refined_deg21.9621124
X-RAY DIFFRACTIONr_angle_other_deg1.0231761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025102
X-RAY DIFFRACTIONr_chiral_restr0.130.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02913
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02152
X-RAY DIFFRACTIONr_nbd_refined0.2430.2194
X-RAY DIFFRACTIONr_nbd_other0.2610.2909
X-RAY DIFFRACTIONr_nbtor_other0.0920.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.40.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.220
X-RAY DIFFRACTIONr_mcbond_it1.3371.5515
X-RAY DIFFRACTIONr_mcangle_it2.3792832
X-RAY DIFFRACTIONr_scbond_it4.1373314
X-RAY DIFFRACTIONr_scangle_it6.4284.5292
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 82
Rwork0.315 1411

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