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- PDB-1gof: NOVEL THIOETHER BOND REVEALED BY A 1.7 ANGSTROMS CRYSTAL STRUCTUR... -

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Basic information

Entry
Database: PDB / ID: 1gof
TitleNOVEL THIOETHER BOND REVEALED BY A 1.7 ANGSTROMS CRYSTAL STRUCTURE OF GALACTOSE OXIDASE
ComponentsGALACTOSE OXIDASE
KeywordsOXIDOREDUCTASE(OXYGEN(A))
Function / homology
Function and homology information


galactose oxidase / galactose oxidase activity / extracellular region / metal ion binding
Similarity search - Function
Galactose oxidase/kelch, beta-propeller / Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Galactose oxidase/kelch, beta-propeller / Coagulation factor 5/8 C-terminal domain, discoidin domain / Kelch / Kelch repeat type 1 / Kelch motif / Coagulation factors 5/8 type C domain (FA58C) profile. ...Galactose oxidase/kelch, beta-propeller / Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Galactose oxidase/kelch, beta-propeller / Coagulation factor 5/8 C-terminal domain, discoidin domain / Kelch / Kelch repeat type 1 / Kelch motif / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / 7 Propeller / Methylamine Dehydrogenase; Chain H / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Jelly Rolls / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / COPPER (II) ION / Galactose oxidase / Galactose oxidase
Similarity search - Component
Biological speciesHypomyces rosellus (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsIto, N. / Phillips, S.E.V. / Knowles, P.F.
Citation
Journal: Nature / Year: 1991
Title: Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase.
Authors: Ito, N. / Phillips, S.E. / Stevens, C. / Ogel, Z.B. / McPherson, M.J. / Keen, J.N. / Yadav, K.D. / Knowles, P.F.
#1: Journal: To be Published
Title: The Crystal Structure of a Free Radical Enzyme, Galactose Oxidase
Authors: Ito, N. / Phillips, S.E.V. / Yadav, K.K.S. / Knowles, P.F.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Galactose Oxidase of Dactylium Dendroides: Gene Cloning and Sequence Analysis
Authors: McPherson, M.J. / Ogel, Z.B. / Stevens, C. / Yadav, K.D.S. / Keen, J.M. / Knowles, P.F.
History
DepositionSep 30, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Remark 700SHEET THE SHEET PRESENTED AS *S9* ON SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S9* ON SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY AN EIGHT-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DOMAIN 3 (RESIDUES 553 - 639) HAS A VERY COMPLICATED HYDROGEN BONDING NETWORK WHICH IS DIFFICULT TO DESCRIBE. IN THE SHEET RECORDS BELOW, THIS IS SIMPLIFIED BY REGARDING SEVERAL PAIRS OF BETA-STRANDS AS ONE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALACTOSE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7855
Polymers68,5791
Non-polymers2074
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.000, 89.400, 86.700
Angle α, β, γ (deg.)90.00, 117.80, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 52 / 2: CIS PROLINE - PRO 163 / 3: CIS PROLINE - PRO 350

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Components

#1: Protein GALACTOSE OXIDASE /


Mass: 68578.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypomyces rosellus (fungus)
References: UniProt: Q01745, UniProt: P0CS93*PLUS, galactose oxidase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Source detailsTHERE IS SOME UNCERTAINTY AS TO THE EXACT TYPING OF THE FUNGUS DACTYLIUM DENDROIDES. (SEE REFERENCE 2).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.80 Macetate1reservoir
2ammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. obs: 57092 / % possible obs: 79.1 % / Num. measured all: 117980 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 52.6 % / Num. unique obs: 5908 / Num. measured obs: 11365

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→10 Å / Rfactor obs: 0.177 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 10 316 5156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor all: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.05

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