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- PDB-1bt2: CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE RED... -

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Basic information

Entry
Database: PDB / ID: 1bt2
TitleCATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE REDUCED CU(I)-CU(I) STATE
ComponentsPROTEIN (CATECHOL OXIDASE)
KeywordsOXIDOREDUCTASE / CATECHOL OXIDASE / DICOPPER ENZYME / IPOMOEA BATATAS
Function / homology
Function and homology information


catechol oxidase / catechol oxidase activity / chloroplast thylakoid lumen / copper ion binding
Similarity search - Function
Polyphenol oxidase, central domain / Polyphenol oxidase, C-terminal / Polyphenol oxidase middle domain / Chloroplastic Polyphenol Oxidase C-terminal domain / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase copper-binding domain ...Polyphenol oxidase, central domain / Polyphenol oxidase, C-terminal / Polyphenol oxidase middle domain / Chloroplastic Polyphenol Oxidase C-terminal domain / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CU-O-CU LINKAGE / Polyphenol oxidase I, chloroplastic
Similarity search - Component
Biological speciesIpomoea batatas (sweet potato)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.7 Å
AuthorsKlabunde, T. / Eicken, C. / Sacchettini, J.C. / Krebs, B.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of a plant catechol oxidase containing a dicopper center.
Authors: Klabunde, T. / Eicken, C. / Sacchettini, J.C. / Krebs, B.
History
DepositionSep 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CATECHOL OXIDASE)
B: PROTEIN (CATECHOL OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9154
Polymers77,6292
Non-polymers2862
Water3,135174
1
A: PROTEIN (CATECHOL OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9582
Polymers38,8151
Non-polymers1431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (CATECHOL OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9582
Polymers38,8151
Non-polymers1431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.250, 162.600, 51.490
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99998, -0.005017, 0.003781), (-0.005078, -0.999855, 0.016274), (0.003699, -0.016293, -0.99986)
Vector: -17.493, 236.77969, 53.7878)

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Components

#1: Protein PROTEIN (CATECHOL OXIDASE) / O-DIPHENOL OXIDASE


Mass: 38814.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COVALENT THIOETHER BOND BETWEEN H109 AND C92 / Source: (natural) Ipomoea batatas (sweet potato) / Organ: MATURE TUBER / References: UniProt: Q9ZP19, catechol oxidase
#2: Chemical ChemComp-C2O / CU-O-CU LINKAGE


Mass: 143.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 ...Details: CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 MM DTT WAS USED TO REDUCE THE ACTIVE SITE., VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
2120 mg/mlPEG60001drop
3500 mM1dropNaCl
450 mMHEPES1drop
5200 mg/mlPEG60001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 18524 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.055 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.8 Å / Rsym value: 0.106 / % possible all: 90.4
Reflection
*PLUS
Num. measured all: 50613 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 90.4 % / Rmerge(I) obs: 0.106

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
MLPHAREphasing
SHARPphasing
DMmodel building
X-PLOR3.1refinement
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→8 Å / σ(F): 3
Details: RESIDUES INVOLVED IN PACKING INTERACTIONS WERE EXCLUDED FROM THE NCS RESTRAINTS.
RfactorNum. reflection% reflection
Rfree0.278 -5 %
Rwork0.184 --
obs0.184 17217 88.3 %
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 6 174 5512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.04
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.09 Å / Weight position: 100
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2

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