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- PDB-1cf9: Structure of the mutant VAL169CYS of catalase HPII from Escherich... -

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Basic information

Entry
Database: PDB / ID: 1cf9
TitleStructure of the mutant VAL169CYS of catalase HPII from Escherichia coli
ComponentsPROTEIN (CATALASE HPII)
KeywordsOXIDOREDUCTASE / HYDROGEN PEROXIDE / 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 / cytoplasm / cytosol
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 / SYNCHROTRON / OTHER / Resolution: 1.8 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: Structure / Year: 1995
Title: Crystal Structure of Catalase HPII from Escherichia Coli
Authors: Bravo, J. / Verdaguer, N. / Tormo, J. / Betzel, C. / Switala, J. / Loewen, P.C. / Fita, I.
#2: Journal: Acta Crystallogr.,Sect.A / Year: 1993
Title: 2.8 A Crystal Structure of Catalase Hpii from Escherichia Coli
Authors: Bravo, J. / Tormo, J. / Verdaguer, N. / Fita, I. / Betzel, C. / Switala, J. / Loewen, P.C.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Catalase Hpii from Escherichia Coli
Authors: Tormo, J. / Fita, I. / Switala, J. / Loewen, P.C.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: The Refined Structure of Beef Liver Catalase at 2.5 A Resolution
Authors: Fita, I. / Silva, A.M. / Murthy, M.R.N. / Rossmann, M.G.
History
DepositionMar 24, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 6, 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 12, 2014Group: Database references / Structure summary
Revision 1.4Mar 14, 2018Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 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_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_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: PROTEIN (CATALASE HPII)
B: PROTEIN (CATALASE HPII)
C: PROTEIN (CATALASE HPII)
D: PROTEIN (CATALASE HPII)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,5688
Polymers337,1024
Non-polymers2,4664
Water48,3882686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58460 Å2
ΔGint-277 kcal/mol
Surface area80030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.470, 133.040, 122.220
Angle α, β, γ (deg.)90.00, 109.64, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(-1), (-1), (1)
2given(-1), (1), (-1)
3given(1), (-1), (-1)

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Components

#1: Protein
PROTEIN (CATALASE HPII)


Mass: 84275.461 Da / Num. of mol.: 4 / Mutation: V169C
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.: 2686 / Source method: isolated from a natural source / Formula: H2O
Sequence details1IPH A SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH B SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH C SWS ...1IPH A SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH B SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH C SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH D SWS P21179 1 - 26 NOT IN ATOMS LIST

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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: 2.4 Å3/Da / Density % sol: 50 %
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9058
DetectorDate: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9058 Å / Relative weight: 1
ReflectionResolution: 1.77→20 Å / Num. obs: 250445 / % possible obs: 88.3 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 9 / Net I/σ(I): 9.6
Reflection shellResolution: 1.77→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 86.7
Reflection shell
*PLUS
% possible obs: 86.7 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: 1IPH

1iph


Resolution: 1.8→20 Å / SU B: 3.62 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.237 -10 %RANDOM
Rwork0.1811 ---
all-240437 --
obs-240437 88.3 %-
Displacement parametersBiso mean: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-2.43 Å20 Å2
2--0 Å23.65 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22976 0 172 2686 25834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.00140.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.1470.159
X-RAY DIFFRACTIONp_mcangle_it0.1640.195
X-RAY DIFFRACTIONp_scbond_it0.1720.159
X-RAY DIFFRACTIONp_scangle_it0.1930.195
X-RAY DIFFRACTIONp_plane_restr0.013
X-RAY DIFFRACTIONp_chiral_restr0.1630.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1760.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.5 Å2
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal target: 0.02

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