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- PDB-1h7k: Formation of a tyrosyl radical intermediate in Proteus mirabilis ... -

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Basic information

Entry
Database: PDB / ID: 1h7k
TitleFormation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity
ComponentsCATALASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (H2O2 ACCEPTOR) / PEROXIDASE / IRON / HEM / HYDROGEN PEROXIDE / NADP
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesPROTEUS MIRABILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAndreoletti, P. / Gambarelli, S. / Gaillard, J. / Sainz, G. / Stojanoff, V. / Jouve, H.M.
Citation
Journal: Biochemistry / Year: 2001
Title: Formation of a Tyrosyl Radical Intermediate in Proteus Mirabilis Catalase by Directed Mutagenesis and Consequences for Nucleotide Reactivity.
Authors: Andreoletti, P. / Gambarelli, S. / Sainz, G. / Stojanoff, V. / White, C. / Desfonds, G. / Gagnon, J. / Gaillard, J. / Jouve, H.M.
#1: 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.
#2: 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.
#3: 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.
#4: 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 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2004Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 13, 2023Group: 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_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)56,3834
Polymers55,6111
Non-polymers7723
Water3,027168
1
A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules

A: CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,53116
Polymers222,4454
Non-polymers3,08612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area46220 Å2
ΔGint-288.6 kcal/mol
Surface area59150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.000, 110.000, 251.200
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-2022-

HOH

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Components

#1: Protein CATALASE


Mass: 55611.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: METHIONINE SULFONE IN POSITION 53, TYROSINE 337 LACK THE HYDROXYL HYDROGEN
Source: (gene. exp.) PROTEUS MIRABILIS (bacteria) / Plasmid: PALTER-CAT-F215Y / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 DE3 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMODRES: 1H7K OMT A 53() METHIONINE SULFONE (S-DIOXYMETHIONINE) MODRES: 1H7K TYR A 337() OXYGEN OF ...MODRES: 1H7K OMT A 53() METHIONINE SULFONE (S-DIOXYMETHIONINE) MODRES: 1H7K TYR A 337() OXYGEN 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: 3.82 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: HANGING DROP AT 4 DEG C, pH 7.30
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9574
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9574 Å / Relative weight: 1
ReflectionResolution: 2.4→29.26 Å / Num. obs: 35932 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 15.8 % / Biso Wilson estimate: 40 Å2
Reflection shellResolution: 2→2.05 Å / % possible all: 94.6
Reflection
*PLUS
Redundancy: 15.8 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.251

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CAE

1cae
PDB Unreleased entry


Resolution: 2.4→29.26 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2727867.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: AMINO ACIDS 358 - 362 ARE NOT REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1794 5 %RANDOM
Rwork0.237 ---
obs0.237 35932 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7587 Å2 / ksol: 0.306189 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.33 Å21.89 Å20 Å2
2--10.33 Å20 Å2
3----20.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 52 168 4083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.36
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.8181.5
X-RAY DIFFRACTIONc_mcangle_it1.1352
X-RAY DIFFRACTIONc_scbond_it1.3252
X-RAY DIFFRACTIONc_scangle_it1.6512.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 464 5.1 %
Rwork0.251 8676 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEM.PARAMHEM.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.36

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