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- PDB-2iqf: Crystal structure of Helicobacter pylori catalase compound I -

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Basic information

Entry
Database: PDB / ID: 2iqf
TitleCrystal structure of Helicobacter pylori catalase compound I
ComponentsCatalase
KeywordsOXIDOREDUCTASE / hydroxoferryl heme / beta barrel
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 / OXYGEN ATOM / Catalase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLoewen, P.C. / Carpena, X. / Fita, I.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations.
Authors: Alfonso-Prieto, M. / Borovik, A. / Carpena, X. / Murshudov, G. / Melik-Adamyan, W. / Fita, I. / Rovira, C. / Loewen, P.C.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalase
B: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9127
Polymers117,5882
Non-polymers1,3245
Water15,925884
1
A: Catalase
B: Catalase
hetero molecules

A: Catalase
B: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,82414
Polymers235,1764
Non-polymers2,64810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area50170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.385, 154.286, 95.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Catalase


Mass: 58794.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: katA / Plasmid: pSO100 / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P77872, catalase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG MME550, 0.1M Sodium citrate, 10mM ZnSO4, 3mM Sodium azide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2003
RadiationMonochromator: SI 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→37 Å / Num. all: 80997 / Num. obs: 74135 / % possible obs: 97.4 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rsym value: 0.084 / Net I/σ(I): 6.4
Reflection shellResolution: 1.86→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 11375 / Rsym value: 0.4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QWL

1qwl


Resolution: 1.86→37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.738 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18845 3928 5 %RANDOM
Rwork0.14847 ---
obs0.15051 74135 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.33 Å2
Refine analyzeLuzzati coordinate error obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.86→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8135 0 92 884 9111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228495
X-RAY DIFFRACTIONr_bond_other_d0.0020.025895
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.96911530
X-RAY DIFFRACTIONr_angle_other_deg1.394314246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84623.589443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.184151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5391557
X-RAY DIFFRACTIONr_chiral_restr0.1080.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021840
X-RAY DIFFRACTIONr_nbd_refined0.2060.21755
X-RAY DIFFRACTIONr_nbd_other0.2030.26348
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24046
X-RAY DIFFRACTIONr_nbtor_other0.0890.24125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2694
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.265
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.2323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.2107
X-RAY DIFFRACTIONr_mcbond_it1.0071.56354
X-RAY DIFFRACTIONr_mcbond_other0.2091.51966
X-RAY DIFFRACTIONr_mcangle_it1.15327980
X-RAY DIFFRACTIONr_scbond_it1.93134362
X-RAY DIFFRACTIONr_scangle_it2.6254.53546
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 265 -
Rwork0.209 5503 -
obs--97.56 %

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