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- PDB-2cah: STRUCTURE OF PROTEUS MIRABILIS PR CATALASE FOR THE NATIVE FORM (E... -

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Basic information

Entry
Database: PDB / ID: 2cah
TitleSTRUCTURE OF PROTEUS MIRABILIS PR CATALASE FOR THE NATIVE FORM (E-FE(III)) COMPLEXED WITH NADPH
ComponentsCATALASE
KeywordsOXIDOREDUCTASE (H2O2 ACCEPTOR) / PEROXIDASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / 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 immune-responsive domain / Catalase-related immune-responsive / Catalase active site ...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 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGouet, P. / Jouve, H.-M. / Dideberg, O.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Crystal Packing of Proteus Mirabilis Pr Catalase
Authors: Jouve, H.M. / Gouet, P. / Boudjada, N. / Buisson, G. / Kahn, R. / Duee, E.
#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
DepositionJul 1, 1996Processing site: BNL
SupersessionJan 11, 1997ID: 1CAF
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0883
Polymers55,7261
Non-polymers1,3622
Water1,67593
1
A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,35312
Polymers222,9054
Non-polymers5,4488
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 area49300 Å2
ΔGint-263 kcal/mol
Surface area55780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.360, 112.360, 249.140
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-487-

HOH

21A-579-

HOH

DetailsTHE CATALASE OF PROTEUS MIRABILIS CRYSTALLIZES IN THE SPACE GROUP P 62 2 2 WITH ONE MONOMER PER ASYMMETRIC UNIT. THIS ENTRY GIVES THE COORDINATES OF ONE MONOMER IN THE CRYSTAL.

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Components

#1: Protein CATALASE


Mass: 55726.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PEROXIDE RESISTANT MUTANT / Source: (natural) Proteus mirabilis (bacteria) / Organ: LIVER / References: UniProt: P42321, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE OXYGEN OH OF THE PROXIMAL TYROSINE 337 IS DEPROTONATED.
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: 4.07 Å3/Da / Density % sol: 63 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4-5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Jouve, H.M., (1991) J.Mol.Biol., 221, 1075.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
127 mg/mlprotein1drop
2100 mMTris-HCl1drop
32.5 %(v/v)glycerol1drop
41 Mammonium sulfate1drop
525 mM1dropKCl
62 Mammonium sulfate1reservoir
750 mM1reservoirKCl
8100 mMTris-HCl1reservoir

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Data collection

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→2.823 Å / Num. obs: 24337 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 2.7→2.82 Å / Rsym value: 0.23 / % possible all: 92.4

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PMC WITH NADPH AT 3.1 A RESOLUTION

Resolution: 2.7→15 Å / σ(F): 2
Details: NEW DATA FROM PROTEUS MIRABILIS PR CATALASE COMPLEXED WITH NADPH HAVE BEEN COLLECTED AT PHOTON FACTORY, TSUKUBA, JAPAN AND THE STRUCTURE IS NOW REFINED TO 2.7 RESOLUTION. THIS STRUCTURE IS ...Details: NEW DATA FROM PROTEUS MIRABILIS PR CATALASE COMPLEXED WITH NADPH HAVE BEEN COLLECTED AT PHOTON FACTORY, TSUKUBA, JAPAN AND THE STRUCTURE IS NOW REFINED TO 2.7 RESOLUTION. THIS STRUCTURE IS SIMILAR TO THE 3.1 A RESOLUTION STRUCTURE DESCRIBED IN REFERENCE 1 OF THIS ENTRY. REFERRING TO THIS ARTICLE, IT CAN BE NOTED THAT THE NADPH IS NOW COMPLETELY DEFINED IN THE CARDS OF ELECTRON DENSITY WHILE THE WATER MOLECULE, HOH 38, DESCRIBED AS MAYBE INVOLVED IN THE OXIDATION OF NADPH TO NADP+ IS NOT OBSERVED. WATER MOLECULES HOH 82 OF COMPOUND I STRUCTURE (2CAF) AND HOH 45 OF COMPOUND II STRUCTURE (2CAG) ARE PRESENT IN EQUIVALENT POSITION AND THE PROTEIN IS LIKELY TO BIND A WATER MOLECULE AT THIS SITE. COORDINATES FOR SIDE CHAINS OF RESIDUES 81, 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 TEMPERATURE FACTOR OF 99.99.
RfactorNum. reflection% reflection
Rwork0.196 --
obs0.196 23830 91 %
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 91 93 4045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.2
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
LS refinement shellResolution: 2.7→2.74 Å
RfactorNum. reflection% reflection
Rwork0.29 934 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3PARNAH1E.DNA

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