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- PDB-8cat: The NADPH binding site on beef liver catalase -

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Basic information

Entry
Database: PDB / ID: 8cat
TitleThe NADPH binding site on beef liver catalase
ComponentsCATALASE
KeywordsOXIDOREDUCTASE / H2O2 ACCEPTOR
Function / homology
Function and homology information


catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process ...catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMurthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Fita, I. / Rossmann, M.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: The NADPH binding site on beef liver catalase.
Authors: Fita, I. / Rossmann, M.G.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: The Refined Structure of Beef Liver Catalase at 2.5 Angstroms Resolution
Authors: Fita, I. / Silva, A.M. / Murthy, M.R.N. / Rossmann, M.G.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1985
Title: The Active Center of Catalase
Authors: Fita, I. / Rossmann, M.G.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of Beef Liver Catalase
Authors: Murthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Rossmann, M.G.
#5: Journal: Kristallografiya / Year: 1981
Title: The Structure of Beef Liver Catalase
Authors: Murthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Rossmann, M.G.
#6: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1981
Title: The Structure of Beef Liver Catalase
Authors: Murthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Rossmann, M.G.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Structure and Heme Environment of Beef Liver Catalase at 2.5 Angstroms Resolution
Authors: Reid III, T.J. / Murthy, M.R.N. / Sicignano, A. / Tanaka, N. / Musick, W.D.L. / Rossmann, M.G.
#8: Journal: J.Mol.Biol. / Year: 1976
Title: Crystalline Bovine Liver Catalase
Authors: Eventoff, W. / Tanaka, N. / Rossmann, M.G.
#9: Journal: J.Mol.Biol. / Year: 1975
Title: The Molecular Symmetry of Bovine Liver Catalase
Authors: Eventoff, W. / Gurskaya, G.V.
History
DepositionNov 15, 1984Processing site: BNL
SupersessionApr 1, 1985ID: 3CAT
Revision 1.0Apr 1, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 1.4Nov 21, 2012Group: Derived calculations
Revision 1.5Nov 1, 2017Group: Derived calculations / Other / Category: pdbx_database_status / pdbx_struct_assembly
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.details ..._pdbx_database_status.process_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_details
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper / struct_site
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[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn_angle.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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] / _struct_ncs_oper.vector[3] / _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 NINE-STRANDED SHEETS S1A AND S1B DESCRIBED BELOW ARE ACTUALLY EIGHT-STRANDED BETA BARRELS. ...SHEET THE NINE-STRANDED SHEETS S1A AND S1B DESCRIBED BELOW ARE ACTUALLY EIGHT-STRANDED BETA BARRELS. THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE
B: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0536
Polymers115,3292
Non-polymers2,7244
Water1,76598
1
A: CATALASE
B: CATALASE
hetero molecules

A: CATALASE
B: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,10512
Polymers230,6584
Non-polymers5,4488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)142.000, 142.000, 103.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUE 405 IS A CIS-PROLINE.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.918275, 0.047185, -0.393099), (0.047184, -0.972758, -0.226956), (-0.393142, -0.226989, 0.891033)
Vector: -58.61394, 179.97282, 9.41719)
DetailsTranslation is required to obtain the tetramer because the coordinates are not presented in standard frame.

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Components

#1: Protein CATALASE


Mass: 57664.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00432, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal grow
*PLUS
pH: 8.8 / Method: unknown
Details: referred to 'Reid /III, T.J.', (1981) Proc.Nat.Acad.Sci.USA, 78, 4767-4771
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 mg/mlcatalase11
21.71 M11NaCl
310 mMTris11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementResolution: 2.5→8.5 Å / Rfactor Rwork: 0.191
Refinement stepCycle: LAST / Resolution: 2.5→8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 182 98 8296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.29
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8.5 Å / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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