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- PDB-1iph: STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1iph
TitleSTRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI
ComponentsCATALASE HPII
KeywordsOXIDOREDUCTASE / HYDROGEN PEROXIDE
Function / homology
Function and homology information


catalase / catalase activity / hyperosmotic response / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / heme binding / DNA damage response / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / 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 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBravo, J. / Loewen, P.C. / Fita, I.
Citation
Journal: Structure / Year: 1995
Title: Crystal structure of catalase HPII from Escherichia coli.
Authors: Bravo, J. / Verdaguer, N. / Tormo, J. / Betzel, C. / Switala, J. / Loewen, P.C. / Fita, I.
#1: Journal: Joint Ccp4 Esf-Eacbm Newsletter on Protein Crystallography
Year: 1993
Title: 2.8 A Crystal Structure of Catalase Hpii from Escherichia Coli
Authors: Bravo, J. / Verdaguer, N. / Tormo, J. / Betzel, C. / Switala, J. / Loewen, P.C. / Fita, I.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Catalase Hpii from Escherichia Coli
Authors: Tormo, J. / Fita, I. / Switala, J. / Loewen, P.C.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: The Refined Structure of Beef Liver Catalase at 2.5 A Resolution
Authors: Fita, I. / Silva, A.M. / Murthy, M.R.N. / Rossmann, M.G.
History
DepositionDec 31, 1995Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 31, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_PDB_matrix / pdbx_struct_conn_angle / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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[3] / _pdbx_struct_conn_angle.value / _pdbx_validate_peptide_omega.omega / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_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] / _struct_ncs_oper.vector[3]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE HPII
B: CATALASE HPII
C: CATALASE HPII
D: CATALASE HPII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,5528
Polymers337,0864
Non-polymers2,4664
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58840 Å2
ΔGint-277 kcal/mol
Surface area80670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.200, 134.700, 124.400
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99901437, 4.573E-5, 0.04438646), (4.209E-5, -0.99999804, 0.00189534), (0.04438917, 0.0020595, 0.99901242)31.30354, 3.43677, -0.69865
2given(-0.97618921, -0.21694447, -0.00032301), (-0.21689666, 0.97618506, 0.00294232), (-0.00030528, 0.00278139, -0.99999586)31.0336, 3.42524, -12.85569
3given(0.97520358, 0.21689874, -0.04406346), (0.21685457, -0.97618702, -0.00483766), (-0.0440839, -0.00484089, -0.99901656)-0.26994, -0.01153, -12.15703

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Components

#1: Protein
CATALASE HPII


Mass: 84271.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Organ: LIVER / References: UniProt: P21179, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %(w/v)PEG33501reservoir
21.5 M1reservoirLiCl
30.2 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 225245 / % possible obs: 90 % / Rmerge(I) obs: 0.108 / Num. measured all: 65329
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.2 / Rfactor obs: 0.2 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22984 0 172 0 23156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.49
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
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 58477
Solvent computation
*PLUS
Displacement parameters
*PLUS

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