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- PDB-4cat: THREE-DIMENSIONAL STRUCTURE OF CATALASE FROM PENICILLIUM VITALE A... -

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Database: PDB / ID: 4cat
TitleTHREE-DIMENSIONAL STRUCTURE OF CATALASE FROM PENICILLIUM VITALE AT 2.0 ANGSTROMS RESOLUTION
ComponentsCATALASE
KeywordsOXIDOREDUCTASE(H2O2(A))
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsVainshtein, B.K. / Melik-Adamyan, W.R. / Barynin, V.V. / Vagin, A.A. / Grebenko, A.I.
Citation
Journal: J.Mol.Biol. / Year: 1986
Title: Three-dimensional structure of catalase from Penicillium vitale at 2.0 A resolution.
Authors: Vainshtein, B.K. / Melik-Adamyan, W.R. / Barynin, V.V. / Vagin, A.A. / Grebenko, A.I. / Borisov, V.V. / Bartels, K.S. / Fita, I. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 1986
Title: Comparison of Beef Liver and Penicillium Vitale Catalases
Authors: Melik-Adamyan, W.R. / Barynin, V.V. / Vagin, A.A. / Borisov, V.V. / Vainshtein, B.K. / Fita, I. / Murthy, M.R.N. / Rossmann, M.G.
#2: Journal: Kristallografiya / Year: 1982
Title: The Mechanism of Crystallization of Proteins in an Ultracentrifuge (Russian)
Authors: Barynin, V.V. / Melik-Adamyan, V.R.
#3: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1982
Title: The Mechanism of Crystallization of Proteins in an Ultracentrifuge
Authors: Barynin, V.V. / Melik-Adamyan, V.R.
#4: Journal: Kristallografiya / Year: 1981
Title: Structure of Penicillium Vitale Catalase (Russian)
Authors: Vainshtein, B.K. / Melik-Adamyan, V.R. / Barynin, V.V. / Vagin, A.A. / Grebenko, A.I.
#5: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1981
Title: Structure of Catalase of Penicillium Vitale
Authors: Vainshtein, B.K. / Melik-Adamyan, W.R. / Barynin, V.V. / Vagin, A.A. / Grebenko, A.I.
#6: Journal: Nature / Year: 1981
Title: Three-Dimensional Structure of the Enzyme Catalase
Authors: Vainshtein, B.K. / Melik-Adamyan, W.R. / Barynin, V.V. / Vagin, A.A. / Grebenko, A.I.
#7: Journal: Dokl.Akad.Nauk Sssr / Year: 1980
Title: X-Ray Diffraction Study of Catalase from Penicillium Vitale at 3.5 Angstroms Resolution (Russian)
Authors: Vainshtein, B.K. / Melik-Adamian, V.R. / Barynin, V.V. / Vagin, A.A.
#8: Journal: Dokl.Biochem.(Engl.Transl.) / Year: 1980
Title: X-Ray Diffraction Investigation of Catalase of Penicillium Vitale with 3.5 Angstroms Resolution
Authors: Vainshtein, B.K. / Melik-Adamyan, V.R. / Barynin, V.V. / Vagin, A.A.
#9: Journal: Dokl.Akad.Nauk Sssr / Year: 1979
Title: X-Ray Study of the Structure of Catalase of Penicillium Vitale Pidopl. Et Bilai with the 6 Angstroms Resolution (Russian)
Authors: Vainstein, B.K. / Melik-Adamian, V.R. / Barynin, V.V. / Vagin, A.A. / Nekrasov, Iu.V. / Malinina, I.V. / Gulyi, M.F. / Gudkova, L.V. / Degtiar, R.G.
#10: Journal: Dokl.Biochem.(Engl.Transl.) / Year: 1979
Title: X-Ray Diffraction Investigation of the Structure of Catalase of the Fungus Penicillium Vitale Pidopl. Et Bilai with a Resolution of 6 Angstroms
Authors: Vainshtein, B.K. / Melik-Adamyan, V.R. / Barynin, V.V. / Vagin, A.A. / Nekrasov, Yu.N. / Malinina, L.V. / Gulyi, M.F. / Gudkova, L.V. / Degtyar, R.G.
#11: Journal: Kristallografiya / Year: 1975
Title: Crystallization of Catalase in an Ultracentrifuge (Russian)
Authors: Karpukhina, S.Ya. / Barynin, V.V. / Lobanova, G.M.
#12: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1975
Title: Crystallization of Catalase in the Ultracentrifuge
Authors: Karpukhina, S.Ya. / Barynin, V.V. / Lobanova, G.M.
History
DepositionFeb 24, 1983Processing site: BNL
Revision 1.0Sep 6, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 31, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_peptide_omega.omega / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Remark 700SHEET THE NINE-STRANDED BETA-SHEET *B1* PRESENTED ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT- ...SHEET THE NINE-STRANDED BETA-SHEET *B1* PRESENTED ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS DENOTED BY HAVING THE FIRST STRAND RECUR AS THE LAST.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: CATALASE
B: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4374
Polymers112,2042
Non-polymers1,2332
Water00
1
A: CATALASE
B: CATALASE
hetero molecules

A: CATALASE
B: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,8758
Polymers224,4094
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)144.400, 144.400, 133.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: SEE REMARK 5.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.571766, -0.247241, -0.782224), (-0.247241, -0.857255, 0.451617), (-0.782328, 0.451677, 0.429021)
Vector: 60.01698, 103.95244)
DetailsPENICILLIUM VITALE CATALASE IS A MOLECULE WITH 222 SYMMETRY. THE ASYMMETRIC UNIT COMPRISES TWO SUBUNITS RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS. COORDINATES FOR ONE SUBUNIT ARE GIVEN IN THIS ENTRY. APPLYING THE TRANSFORMATION GIVEN ON THE MTRIX RECORDS BELOW WILL GENERATE COORDINATES FOR THE OTHER HALF OF THE ASYMMETRIC UNIT.

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Components

#1: Protein CATALASE


Mass: 56102.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium janthinellum (fungus) / References: catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Nonpolymer detailsTHERE IS SOME EVIDENCE THAT THE HEME OF THIS CATALASE IS UNUSUAL AND THE PROTOPORPHYRIN IX ...THERE IS SOME EVIDENCE THAT THE HEME OF THIS CATALASE IS UNUSUAL AND THE PROTOPORPHYRIN IX COORDINATES IN THIS ENTRY ARE TENTATIVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.73 %

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Processing

RefinementHighest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 86 0 5360

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