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- PDB-1bt3: CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NAT... -

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Basic information

Entry
Database: PDB / ID: 1bt3
TitleCATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 20, 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9582
Polymers38,8151
Non-polymers1431
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.120, 156.750, 56.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 38814.582 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Cu2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
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., ...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., 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: 291 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: 2.5→20 Å / Num. obs: 13446 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.084 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.6 Å / Rsym value: 0.226 / % possible all: 85.9
Reflection
*PLUS
Num. measured all: 47548 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 85.9 % / Rmerge(I) obs: 0.226

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.25 -5 %
Rwork0.167 --
obs0.167 12028 84.6 %
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 3 82 2751
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.81
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
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 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.4 Å2

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