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- PDB-1qwl: Structure of Helicobacter pylori catalase -

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Basic information

Entry
Database: PDB / ID: 1qwl
TitleStructure of Helicobacter pylori catalase
ComponentsKatA catalase
KeywordsOXIDOREDUCTASE / beta barrel / azide complex / oxyferryl complex
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 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
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Catalase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLoewen, P.C. / Carpena, X. / Perez-Luque, R. / Rovira, C. / Haas, R. / Obenbreit, S. / Nicholls, P. / Fita, I.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of Helicobacter pylori Catalase, with and without Formic Acid Bound, at 1.6 A Resolution
Authors: Loewen, P.C. / Carpena, X. / Rovira, C. / Ivanich, A. / Perez-Luque, R. / Haas, R. / Obenbreit, S. / Nicholls, P. / Fita, I.
History
DepositionSep 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim / 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_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KatA catalase
B: KatA catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7676
Polymers117,4602
Non-polymers1,3074
Water18,1051005
1
A: KatA catalase
B: KatA catalase
hetero molecules

A: KatA catalase
B: KatA catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,53412
Polymers234,9204
Non-polymers2,6148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area49900 Å2
ΔGint-275 kcal/mol
Surface area57830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.264, 154.502, 95.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1814-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 1 - 491 / Label seq-ID: 1 - 491

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein KatA catalase


Mass: 58730.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: katA (hp0875) / Plasmid: pSO100 / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P77872, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1005 / Source method: isolated from a natural source / Formula: H2O

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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: 39.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG MME 550, 0.1 M sodium citrate, 10 mM ZnSO4, 3 mM NaN3, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
215 %PEG550 MME1reservoir
30.1 Msodium citrate1reservoirpH5.6
410 mM1reservoirZnSO4
53 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2002
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.6→29.5 Å / Num. all: 119267 / Num. obs: 113241 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.06 / Net I/σ(I): 13.6
Reflection shellResolution: 1.6→1.69 Å / Num. unique all: 7699 / Rsym value: 0.137 / % possible all: 87.3
Reflection
*PLUS
Num. obs: 119258 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 87.3 % / Num. unique obs: 7699 / Rmerge(I) obs: 0.137

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human erythrocyte catalase

Resolution: 1.6→28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.286 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22854 6018 5 %RANDOM
Rwork0.18089 ---
all0.1812 119267 --
obs0.18331 113241 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8058 0 91 1005 9154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0218480
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.95811510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835982
X-RAY DIFFRACTIONr_chiral_restr0.1320.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026668
X-RAY DIFFRACTIONr_nbd_refined0.220.24114
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.2426
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.2141
X-RAY DIFFRACTIONr_mcbond_it1.1171.54919
X-RAY DIFFRACTIONr_mcangle_it1.52127979
X-RAY DIFFRACTIONr_scbond_it2.59733561
X-RAY DIFFRACTIONr_scangle_it3.5534.53531
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4040 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.235
loose thermal1.3410
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 362
Rwork0.229 7337
Refinement
*PLUS
Rfactor Rfree: 0.219 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8
X-RAY DIFFRACTIONr_plane_restr0.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.28 / Rfactor Rwork: 0.22

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