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- PDB-1ng3: Complex of ThiO (glycine oxidase) with acetyl-glycine -

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Basic information

Entry
Database: PDB / ID: 1ng3
TitleComplex of ThiO (glycine oxidase) with acetyl-glycine
ComponentsGlycine oxidase
KeywordsOXIDOREDUCTASE / Flavoprotein / oxidase
Function / homology
Function and homology information


glycine oxidase / glycine oxidase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / amino acid metabolic process / response to herbicide / FAD binding / oxidoreductase activity / cytoplasm
Similarity search - Function
Glycine oxidase ThiO / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYLAMINO-ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Glycine oxidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSettembre, E.C. / Dorrestein, P.C. / Park, J. / Augustine, A. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2003
Title: Structural and Mechanistic Studies on ThiO, a Glycine Oxidase Essential for Thiamin Biosynthesis in Bacillus subtilis
Authors: Settembre, E.C. / Dorrestein, P.C. / Park, J. / Augustine, A. / Begley, T.P. / Ealick, S.E.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE ACCORDING TO THE AUTHOR, ALA 288 MAY HAVE BEEN MUTATED ACCIDENTALLY TO PRO DUE TO PCR ERROR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine oxidase
B: Glycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9997
Polymers87,0992
Non-polymers1,9005
Water1,928107
1
A: Glycine oxidase
B: Glycine oxidase
hetero molecules

A: Glycine oxidase
B: Glycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,99914
Polymers174,1984
Non-polymers3,80110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area16710 Å2
ΔGint-60 kcal/mol
Surface area51110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.378, 139.378, 208.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the two-fold axis: -Y,-X,-Z+5/6.

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Components

#1: Protein Glycine oxidase


Mass: 43549.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: GOXB / Plasmid: pET16-b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: O31616, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-AAC / ACETYLAMINO-ACETIC ACID


Mass: 117.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.52 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.15
Details: PEG MME 2000, HEPES, pH 7.15, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
218 %PEG2000 MME1reservoir
3100 mMHEPES1reservoirpH7.15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 35731 / Num. obs: 35656 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.068
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 34445 / Num. measured all: 164553 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
CNS1refinement
Adxvdata processing
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD Phased Structure of ThiO

Resolution: 2.6→49.17 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1905 5.3 %RANDOM
Rwork0.208 ---
obs0.208 35656 95.3 %-
all-37377 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2803 Å2 / ksol: 0.360635 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.54 Å26.19 Å20 Å2
2---4.54 Å20 Å2
3---9.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 127 107 5926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 128 2.2 %
Rwork0.271 5779 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3AAC.PARAMFAD.TOP
X-RAY DIFFRACTION4FAD.PARAMAAC.TOP
X-RAY DIFFRACTION5PO4_FIX.PARAMPO4_FIX.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / % reflection Rfree: 6 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41

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