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- PDB-1r6y: Crystal structure of YgiN from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1r6y
TitleCrystal structure of YgiN from Escherichia coli
ComponentsProtein ygiN
KeywordsStructural genomics / Unknown function / hypothetical protein / functional annotation / ferredoxin-like fold / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


response to acidic pH / Oxidoreductases / 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
Probable quinol monooxygenase YgiN / Probable quinol monooxygenase YgiN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsAdams, M.A. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
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
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ygiN


Theoretical massNumber of molelcules
Total (without water)12,9051
Polymers12,9051
Non-polymers00
Water3,333185
1
A: Protein ygiN

A: Protein ygiN


Theoretical massNumber of molelcules
Total (without water)25,8102
Polymers25,8102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area2720 Å2
ΔGint-20 kcal/mol
Surface area10450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.057, 102.057, 102.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Protein ygiN


Mass: 12904.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40718, UniProt: P0ADU2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium Sulphate, Tri-Sodium Citrate, Sodium/Potassium Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F111.199998
SYNCHROTRONNSLS X9A20.979383, 0.979228, 0.971708
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 25, 2002
MARRESEARCH2CCDApr 11, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rh-coated Si MirrorsSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1999981
20.9793831
30.9792281
40.9717081
ReflectionResolution: 2.2→50 Å / Num. all: 9700 / Num. obs: 9700 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 3.944 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.2 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24948 467 4.8 %RANDOM
Rwork0.20842 ---
all0.21031 9700 --
obs0.21031 9700 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: 37.566 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 0 0 185 982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.040.021814
X-RAY DIFFRACTIONr_bond_other_d0.0020.02748
X-RAY DIFFRACTIONr_angle_refined_deg2.331.9421103
X-RAY DIFFRACTIONr_angle_other_deg1.03731745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9515102
X-RAY DIFFRACTIONr_chiral_restr0.1530.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02896
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02147
X-RAY DIFFRACTIONr_nbd_refined0.2690.202161
X-RAY DIFFRACTIONr_nbd_other0.2560.2830
X-RAY DIFFRACTIONr_nbtor_other0.1020.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4450.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.24
X-RAY DIFFRACTIONr_mcbond_it1.6661.5514
X-RAY DIFFRACTIONr_mcangle_it3.0122831
X-RAY DIFFRACTIONr_scbond_it4.663300
X-RAY DIFFRACTIONr_scangle_it7.5514.5272
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.222 40
Rwork0.231 646

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