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- PDB-1k3i: Crystal Structure of the Precursor of Galactose Oxidase -

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Basic information

Entry
Database: PDB / ID: 1k3i
TitleCrystal Structure of the Precursor of Galactose Oxidase
ComponentsGalactose Oxidase Precursor
KeywordsOXIDOREDUCTASE / 7 Blade Beta Propeller / Prosequence Form / Precursor of Copper Enzyme.
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 motif / Kelch repeat type 1 / 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 motif / Kelch repeat type 1 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / alpha-D-glucopyranose / : / Galactose oxidase
Similarity search - Component
Biological speciesFusarium sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFirbank, S.J. / Rogers, M.S. / Wilmot, C.M. / Dooley, D.M. / Halcrow, M.A. / Knowles, P.F. / McPherson, M.J. / Phillips, S.E.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the precursor of galactose oxidase: an unusual self-processing enzyme.
Authors: Firbank, S.J. / Rogers, M.S. / Wilmot, C.M. / Dooley, D.M. / Halcrow, M.A. / Knowles, P.F. / McPherson, M.J. / Phillips, S.E.
History
DepositionOct 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactose Oxidase Precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7016
Polymers70,3231
Non-polymers3785
Water12,322684
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.313, 89.516, 93.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galactose Oxidase Precursor / E.C.1.1.3.9


Mass: 70322.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium sp. (fungus) / Plasmid: pGOF101 / Production host: Emericella nidulans (mold) / Strain (production host): G191
References: GenBank: 167226, UniProt: P0CS93*PLUS, galactose oxidase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 8000, Sodium MES, Calcium Acetate., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG80001reservoir
2200 mMcalcium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONSRS PX9.620.87
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEMay 28, 1999Yale mirrors
ADSC QUANTUM 42CCDOct 20, 1999Rh coated silicon mirror,single crystal Si(111) monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2Rh coated silicon mirror,single crystal Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.871
ReflectionResolution: 1.4→64 Å / Num. all: 115006 / Num. obs: 115006 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.042 / Net I/σ(I): 72.3
Reflection shellResolution: 1.4→1.49 Å / Mean I/σ(I) obs: 28.5 / Rsym value: 0.092 / % possible all: 93.7
Reflection
*PLUS
Lowest resolution: 64 Å / Num. measured all: 731202 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 93.7 % / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GOG

1gog


Resolution: 1.4→40.41 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2034865.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.193 11573 10.1 %RANDOM
Rwork0.176 ---
all0.176 115416 --
obs0.176 114564 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9577 Å2 / ksol: 0.335113 e/Å3
Displacement parametersBiso mean: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.76 Å20 Å2
3---1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.4→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 19 684 5626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.22 1925 10.6 %
Rwork0.186 16305 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NEWION.PARAMNEWION.PARAM
X-RAY DIFFRACTION4LIGAND.PARAMLIGAND.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
LS refinement shell
*PLUS
Rfactor Rfree: 0.22 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.186

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