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- PDB-3wjs: Crystal structure of GYE (old yellow enzyme) -

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Basic information

Entry
Database: PDB / ID: 3wjs
TitleCrystal structure of GYE (old yellow enzyme)
ComponentsNADH oxidase
KeywordsOXIDOREDUCTASE ACTIVATOR / G oxydans / old yellow protein / C=C oxydation
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alkene reductase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsYuan, Y.A. / Yin, B.
CitationJournal: To be Published
Title: Crystal structure of GYE (old yellow enzyme)
Authors: Yuan, Y.A. / Yin, B.
History
DepositionOct 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7444
Polymers39,2871
Non-polymers4573
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NADH oxidase
hetero molecules

A: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4888
Polymers78,5742
Non-polymers9146
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area3880 Å2
ΔGint-47 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.886, 138.886, 145.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NADH oxidase


Mass: 39287.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: nox / Production host: Escherichia coli (E. coli) / References: UniProt: A1E8I9
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
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: 5.14 Å3/Da / Density % sol: 76.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, KCl, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 12332 / Num. obs: 12332 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 23.1 %
Reflection shellResolution: 3.3→3.36 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.3→46.34 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.856 / SU B: 28.56 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24514 630 4.9 %RANDOM
Rwork0.17405 ---
obs0.17726 12332 99.89 %-
all-12332 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.038 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å21.44 Å2-0 Å2
2--1.44 Å2-0 Å2
3----4.68 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 18 0 2422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192475
X-RAY DIFFRACTIONr_bond_other_d0.0020.022366
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9563358
X-RAY DIFFRACTIONr_angle_other_deg0.92535437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1375314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07723.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.38715387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9351520
X-RAY DIFFRACTIONr_chiral_restr0.0970.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.298→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 51 -
Rwork0.251 869 -
obs--99.46 %
Refinement TLS params.Method: refined / Origin x: -43.719 Å / Origin y: 46.4215 Å / Origin z: -10.5741 Å
111213212223313233
T0.0332 Å2-0.044 Å20.0059 Å2-0.0687 Å2-0.006 Å2--0.0042 Å2
L0.3582 °20.2878 °20.0145 °2-0.5059 °2-0.0037 °2--0.5163 °2
S0.0094 Å °-0.0152 Å °0.0311 Å °0.0068 Å °-0.0117 Å °0.0211 Å °0.0174 Å °0.0211 Å °0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 315
2X-RAY DIFFRACTION1A401 - 402

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