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- PDB-1qf7: STRUCTURE OF THE MUTANT HIS392GLN OF CATALASE HPII FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1qf7
TitleSTRUCTURE OF THE MUTANT HIS392GLN OF CATALASE HPII FROM E. COLI
ComponentsPROTEIN (CATALASE HPII)
KeywordsOXIDOREDUCTASE / COVALENT MODIFICATIONS
Function / homology
Function and homology information


catalase / catalase activity / hyperosmotic response / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / heme binding / DNA damage response / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / 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 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.2 Å
AuthorsMate, M.J. / Loewen, P.C. / Fita, I.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Mutants that alter the covalent structure of catalase hydroperoxidase II from Escherichia coli.
Authors: Mate, M.J. / Sevinc, M.S. / Hu, B. / Bujons, J. / Bravo, J. / Switala, J. / Ens, W. / Loewen, P.C. / Fita, I.
#1: Journal: Proteins / Year: 1999
Title: Structure of catalase HPII from Escherichia coli at 1.9 A resolution.
Authors: Bravo, J. / Mate, M.J. / Schneider, T. / Switala, J. / Wilson, K. / Loewen, P.C. / Fita, I.
History
DepositionMar 26, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 26, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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: PROTEIN (CATALASE HPII)
B: PROTEIN (CATALASE HPII)
C: PROTEIN (CATALASE HPII)
D: PROTEIN (CATALASE HPII)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,5128
Polymers337,0464
Non-polymers2,4664
Water48,2622679
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58930 Å2
ΔGint-274 kcal/mol
Surface area79210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.400, 132.920, 121.670
Angle α, β, γ (deg.)90.00, 109.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (CATALASE HPII)


Mass: 84261.438 Da / Num. of mol.: 4 / Mutation: H392Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PAMKATE72 / Gene (production host): KATE / Production host: Escherichia coli (E. coli) / References: UniProt: P21179, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2679 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growpH: 9 / Details: pH 9
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop / Details: Bravo, J., (1995) Structure, 3, 491.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %(w/v)PEG33501reservoir
21.5 M1reservoirLiCl
30.2 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Oct 1, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.12→20 Å / Num. obs: 137604 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.25 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
CCP4SUITEmodel building
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1IPH

1iph


Resolution: 2.2→20 Å / SU B: 5.565 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.21 -5 %RANDOM
Rwork0.144 ---
obs-137582 96.6 %-
Displacement parametersBiso mean: 13.55 Å2
Baniso -1Baniso -2Baniso -3
1--4.45 Å2-0.72 Å20 Å2
2--0 Å25.165 Å2
3---1.056 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22976 0 172 2679 25827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.6822
X-RAY DIFFRACTIONp_mcangle_it3.0733
X-RAY DIFFRACTIONp_scbond_it4.1552
X-RAY DIFFRACTIONp_scangle_it5.0653
X-RAY DIFFRACTIONp_plane_restr0.014
X-RAY DIFFRACTIONp_chiral_restr0.1530.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1760.3
X-RAY DIFFRACTIONp_planar_tor5.17
X-RAY DIFFRACTIONp_staggered_tor16.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.144 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg16.1

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