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- PDB-4e37: Crystal Structure of P. aeruginosa catalase, KatA tetramer -

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Basic information

Entry
Database: PDB / ID: 4.0E+37
TitleCrystal Structure of P. aeruginosa catalase, KatA tetramer
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Catalase
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, 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 / Chem-NDP / Catalase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsVanderWielen, B.D. / Wilson, J.J. / Kovall, R.A.
CitationJournal: To be Published
Title: KatA, the Major Catalase in Pseudomonas aeruginosa, Assists in Protecting Anaerobic Bacteria From Metabolic and Exogenous Nitric Oxide
Authors: Su, S. / Wilson, J.J. / Panmanee, W. / Makris, T. / Lipscomb, J.D. / Kim, S. / Cho, Y. / Irvin, R.T. / VanderWielen, B.D. / Kovall, R.A. / Hassett, D.J.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,86812
Polymers223,4214
Non-polymers5,4488
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50200 Å2
ΔGint-266 kcal/mol
Surface area57320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.733, 167.427, 90.547
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN C AND (RESSEQ 4:53 OR RESSEQ 55:68 OR RESSEQ...
211CHAIN A AND (RESSEQ 4:53 OR RESSEQ 55:68 OR RESSEQ...
311CHAIN B AND (RESSEQ 4:53 OR RESSEQ 55:68 OR RESSEQ...
411CHAIN D AND (RESSEQ 4:53 OR RESSEQ 55:68 OR RESSEQ...

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Components

#1: Protein
Catalase


Mass: 55855.152 Da / Num. of mol.: 4 / Fragment: KatA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: katA, PA4236 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52762, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 0.1 M sodium acetate, 16% PEG 3350, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 61328 / Num. obs: 61328 / % possible obs: 99.3 % / Observed criterion σ(F): 4.8 / Observed criterion σ(I): 4.8 / Redundancy: 4.1 % / Rsym value: 0.086 / Net I/σ(I): 15.58
Reflection shellResolution: 2.53→2.64 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.15 / Rsym value: 0.263 / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_918)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M85

1m85


Resolution: 2.53→43.462 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 3107 5.07 %
Rwork0.1743 --
obs0.1757 61323 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1281 Å2-0 Å20.0503 Å2
2---1.1961 Å20 Å2
3----1.0063 Å2
Refinement stepCycle: LAST / Resolution: 2.53→43.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15675 0 364 486 16525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01516573
X-RAY DIFFRACTIONf_angle_d1.23222592
X-RAY DIFFRACTIONf_dihedral_angle_d14.3566130
X-RAY DIFFRACTIONf_chiral_restr0.0722249
X-RAY DIFFRACTIONf_plane_restr0.0053067
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C3758X-RAY DIFFRACTIONPOSITIONAL
12A3758X-RAY DIFFRACTIONPOSITIONAL0.172
13B3758X-RAY DIFFRACTIONPOSITIONAL0.181
14D3758X-RAY DIFFRACTIONPOSITIONAL0.186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.57430.27291280.20862231X-RAY DIFFRACTION84
2.5743-2.61650.27211430.212662X-RAY DIFFRACTION99
2.6165-2.66160.27271260.21262667X-RAY DIFFRACTION99
2.6616-2.710.25061280.2112674X-RAY DIFFRACTION99
2.71-2.76210.28961400.21212651X-RAY DIFFRACTION99
2.7621-2.81850.25151360.21342675X-RAY DIFFRACTION100
2.8185-2.87980.23551370.20992633X-RAY DIFFRACTION99
2.8798-2.94670.25811470.21032707X-RAY DIFFRACTION100
2.9467-3.02040.21931500.20952640X-RAY DIFFRACTION100
3.0204-3.1020.25941260.20282664X-RAY DIFFRACTION100
3.102-3.19330.23851350.20172677X-RAY DIFFRACTION100
3.1933-3.29630.22211480.19472664X-RAY DIFFRACTION100
3.2963-3.41410.22031280.20182709X-RAY DIFFRACTION100
3.4141-3.55070.19591380.18922695X-RAY DIFFRACTION100
3.5507-3.71230.2621300.19032461X-RAY DIFFRACTION92
3.7123-3.90790.16921460.16392667X-RAY DIFFRACTION100
3.9079-4.15250.16981630.14912673X-RAY DIFFRACTION100
4.1525-4.47280.15171510.13392665X-RAY DIFFRACTION100
4.4728-4.92240.14841480.12172686X-RAY DIFFRACTION100
4.9224-5.63340.13981600.13612698X-RAY DIFFRACTION100
5.6334-7.09250.16691340.14412704X-RAY DIFFRACTION100
7.0925-43.46830.15031650.13772713X-RAY DIFFRACTION100

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