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- PDB-1ryi: STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE -

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Basic information

Entry
Database: PDB / ID: 1ryi
TitleSTRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE
ComponentsGLYCINE OXIDASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / OXIDASE / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


glycine oxidase / glycine oxidase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / response to herbicide / amino acid metabolic process / 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
FLAVIN-ADENINE DINUCLEOTIDE / GLYCOLIC ACID / Glycine oxidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsMoertl, M. / Diederichs, K. / Welte, W. / Pollegioni, L. / Molla, G. / Motteran, L. / Andriolo, G. / Pilone, M.S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure-function correlation in glycine oxidase from Bacillus subtilis
Authors: Moertl, M. / Diederichs, K. / Welte, W. / Molla, G. / Motteran, L. / Andriolo, G. / Pilone, M.S. / Pollegioni, L.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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: GLYCINE OXIDASE
B: GLYCINE OXIDASE
C: GLYCINE OXIDASE
D: GLYCINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,99312
Polymers170,5474
Non-polymers3,4468
Water18,8441046
1
A: GLYCINE OXIDASE
B: GLYCINE OXIDASE
hetero molecules

A: GLYCINE OXIDASE
B: GLYCINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,99312
Polymers170,5474
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
2
C: GLYCINE OXIDASE
D: GLYCINE OXIDASE
hetero molecules

C: GLYCINE OXIDASE
D: GLYCINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,99312
Polymers170,5474
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Unit cell
Length a, b, c (Å)73.713, 218.765, 217.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsTHE BIOLOGICAL ASSEMBLY IS A TETRAMER. THERE ARE TWO DIFFERENT TETRAMERS IN THE CRYSTAL. THE SECOND PART OF THE FIRST TETRAMER, WICH IS COMPOSED OF CHAIN A AND B AND IT'S SYMMETRY EQUIVALENTS, IS GENERATED BY THE TWO FOLD AXIS x, -y+2, -z+2. THE SECOND PART OF THE SECOND TETRAMER, WICH IS COMPOSED OF CHAIN C AND D AND IT'S SYMMETRY EQUIVALENTS, IS GENERATED BY THE TWO FOLD AXIS -x, y, -z+3/2.

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Components

#1: Protein
GLYCINE OXIDASE / / E.C.1.4.3.19


Mass: 42636.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: GOXB, BSU11670 / Plasmid: PT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) pLYS / References: UniProt: O31616, glycine oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.46 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 10% w/v PEG 1000, 100 mM Imidazole, 200 mM Ca-Acetate, 30 mM Sodium-Glycolate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.97934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2003
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→19.92 Å / Num. all: 159578 / Num. obs: 159578 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.9 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
SOLVEphasing
REFMAC5.1.25refinement
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→19.92 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.782 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21399 8006 5 %RANDOM
Rwork0.17697 ---
obs0.17881 151571 98.31 %-
all-159578 --
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: 25.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11442 0 232 1046 12720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111982
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210634
X-RAY DIFFRACTIONr_angle_refined_deg1.321.96716230
X-RAY DIFFRACTIONr_angle_other_deg0.831324742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2851464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.21702
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213318
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022494
X-RAY DIFFRACTIONr_nbd_refined0.1910.22128
X-RAY DIFFRACTIONr_nbd_other0.2360.211752
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.26367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2660
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.2113
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.88947228
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.122611538
X-RAY DIFFRACTIONr_scbond_it4.87684754
X-RAY DIFFRACTIONr_scangle_it7.174164692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 573
Rwork0.254 10746

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