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- PDB-2cag: CATALASE COMPOUND II -

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Basic information

Entry
Database: PDB / ID: 2cag
TitleCATALASE COMPOUND II
ComponentsCATALASE COMPOUND II
KeywordsOXIDOREDUCTASE (H2O2 ACCEPTOR) / PEROXIDASE / IRON / HEME / HYDROGEN PEROXIDE / NADP
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGouet, P. / Jouve, H.M. / Hajdu, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy.
Authors: Gouet, P. / Jouve, H.M. / Williams, P.A. / Andersson, I. / Andreoletti, P. / Nussaume, L. / Hajdu, J.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal Structure of Proteus Mirabilis Pr Catalase with and without Bound Nadph
Authors: Gouet, P. / Jouve, H.M. / Dideberg, O.
#2: 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.
History
DepositionJun 12, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATALASE COMPOUND II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3432
Polymers55,7261
Non-polymers6161
Water1,26170
1
A: CATALASE COMPOUND II
hetero molecules

A: CATALASE COMPOUND II
hetero molecules

A: CATALASE COMPOUND II
hetero molecules

A: CATALASE COMPOUND II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,3718
Polymers222,9054
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area44760 Å2
ΔGint-256 kcal/mol
Surface area57720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)111.840, 111.840, 249.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

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Components

#1: Protein CATALASE COMPOUND II


Mass: 55726.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMPOUND II WAS OBTAINED BY REDUCING A CRYSTAL CONTAINING THE PROTEIN IN THE COMPOUND I STATE WITH DITHIOTHREITOL
Source: (natural) Proteus mirabilis (bacteria) / Organ: LIVER / Variant: PEROXIDE RESISTANT MUTANT / References: UniProt: P42321, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsOXYGEN OF THE PROXIMAL TYROSINE 337 IS DEPROTONATED.

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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: 4.05 Å3/Da / Density % sol: 63 %
Crystal grow
*PLUS
Temperature: 4-5 ℃ / pH: 7.5 / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
154 mg/mlcatalase1drop
2100 mMTris-HCl1drop
35 %(v/v)glycerol1drop
42 Mammonium sulfate1reservoir
550 mM1reservoirKCl
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: FILM / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 19251 / % possible obs: 73 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.42 / % possible all: 75
Reflection
*PLUS
Num. measured all: 39971
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CAE

2cae
PDB Unreleased entry


Resolution: 2.7→15 Å / Cross valid method: FREE R / σ(F): 2
Details: COORDINATES FOR RESIDUES 1 - 3 AND 479 - 484 ARE NOT INCLUDED. COORDINATES FOR SIDE CHAINS OF RESIDUES 204, 395, 451 AND 72, 450, 473 ARE NOT OBSERVED BEYOND CARBON CB AND CG RESPECTIVELY ...Details: COORDINATES FOR RESIDUES 1 - 3 AND 479 - 484 ARE NOT INCLUDED. COORDINATES FOR SIDE CHAINS OF RESIDUES 204, 395, 451 AND 72, 450, 473 ARE NOT OBSERVED BEYOND CARBON CB AND CG RESPECTIVELY AND MODELED WITH AN OCCUPANCY OF 0.00 AND A BFACTOR OF 99.99.
RfactorNum. reflection% reflection
Rfree0.241 1731 7 %
Rwork0.179 --
obs0.179 17603 68 %
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 43 70 3974
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_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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 file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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