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- PDB-1ye9: Crystal structure of proteolytically truncated catalase HPII from... -

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Basic information

Entry
Database: PDB / ID: 1ye9
TitleCrystal structure of proteolytically truncated catalase HPII from E. coli
Components(catalase HPII) x 2
KeywordsOXIDOREDUCTASE / catalase HPII / proteolytic truncation / beta barrel core
Function / homology
Function and homology information


catalase / hyperosmotic response / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / DNA damage response / heme binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Catalase HPII, helical domain / catalase hpii fold / catalase hpii domain / Catalase hpii, N-terminal domain-like / Helicase, Ruva Protein; domain 3 / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Catalase haem-binding site ...Catalase HPII, helical domain / catalase hpii fold / catalase hpii domain / Catalase hpii, N-terminal domain-like / Helicase, Ruva Protein; domain 3 / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical 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 / Class I glutamine amidotransferase-like / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLoewen, P.C. / Chelikani, P. / Carpena, X. / Fita, I. / Perez-Luque, R. / Donald, L.J. / Switala, J. / Duckworth, H.W.
CitationJournal: Biochemistry / Year: 2005
Title: Characterization of a Large Subunit Catalase Truncated by Proteolytic Cleavage(,)
Authors: Chelikani, P. / Carpena, X. / Perez-Luque, R. / Donald, L.J. / Duckworth, H.W. / Switala, J. / Fita, I. / Loewen, P.C.
History
DepositionDec 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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.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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: catalase HPII
E: catalase HPII
B: catalase HPII
F: catalase HPII
C: catalase HPII
G: catalase HPII
D: catalase HPII
H: catalase HPII
I: catalase HPII
M: catalase HPII
J: catalase HPII
N: catalase HPII
K: catalase HPII
O: catalase HPII
L: catalase HPII
P: catalase HPII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,56624
Polymers445,50616
Non-polymers5,0608
Water3,243180
1
A: catalase HPII
E: catalase HPII
B: catalase HPII
F: catalase HPII
C: catalase HPII
G: catalase HPII
D: catalase HPII
H: catalase HPII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,28312
Polymers222,7538
Non-polymers2,5304
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area91390 Å2
ΔGint-487 kcal/mol
Surface area55310 Å2
MethodPISA
2
I: catalase HPII
M: catalase HPII
J: catalase HPII
N: catalase HPII
K: catalase HPII
O: catalase HPII
L: catalase HPII
P: catalase HPII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,28312
Polymers222,7538
Non-polymers2,5304
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area91560 Å2
ΔGint-490 kcal/mol
Surface area55320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.011, 152.888, 135.287
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51I
61J
71K
81L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 75 - 564 / Label seq-ID: 1 - 256

Dom-IDAuth asym-IDLabel asym-ID
1A - EA - B
2B - FC - D
3C - GE - F
4D - HG - H
5I - MI - J
6J - NK - L
7K - OM - N
8L - PO - P
DetailsBiological unit is a tetramer and the asymmetric unit is composed of two truncated tetramers in which each monomer is cut into two fragments.

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Components

#1: Protein
catalase HPII


Mass: 25615.742 Da / Num. of mol.: 8 / Fragment: proteolytic fragment, residues 75-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MP180 / Gene: KATE / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P21179, catalase
#2: Protein
catalase HPII


Mass: 30072.516 Da / Num. of mol.: 8 / Fragment: proteolytic fragment, residues 309-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MP180 / Gene: KATE / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / References: UniProt: P21179, catalase
#3: Chemical
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.56 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM TrisHCl, 8% PEG 20000, 8% PEG MME 550, 0.2M KSCN, 0.1M dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 18, 2003 / Details: Mirrors
RadiationMonochromator: Diamond(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 109986 / Num. obs: 104927 / % possible obs: 95.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.106 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1 / Num. unique all: 7510 / Rsym value: 0.65 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1GGE

1gge


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.865 / SU B: 20.105 / SU ML: 0.378 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26902 5289 5 %RANDOM
Rwork0.21713 ---
all0.248 109968 --
obs0.21977 99638 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: 43.725 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å22.66 Å2
2---2.62 Å20 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31183 0 352 180 31715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02132563
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.94344390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41153816
X-RAY DIFFRACTIONr_chiral_restr0.1040.24485
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0226260
X-RAY DIFFRACTIONr_nbd_refined0.2820.216371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.21385
X-RAY DIFFRACTIONr_metal_ion_refined0.1730.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4490.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3810.23
X-RAY DIFFRACTIONr_mcbond_it1.0361.519173
X-RAY DIFFRACTIONr_mcangle_it1.926231092
X-RAY DIFFRACTIONr_scbond_it3.184313390
X-RAY DIFFRACTIONr_scangle_it5.0194.513298
Refine LS restraints NCS

Ens-ID: 1 / Number: 3851 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.140.05
2Btight positional0.140.05
3Ctight positional0.140.05
4Dtight positional0.140.05
5Itight positional0.160.05
6Jtight positional0.140.05
7Ktight positional0.160.05
8Ltight positional0.150.05
1Atight thermal0.510.5
2Btight thermal0.410.5
3Ctight thermal0.460.5
4Dtight thermal0.420.5
5Itight thermal0.490.5
6Jtight thermal0.430.5
7Ktight thermal0.510.5
8Ltight thermal0.410.5
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.42 361
Rwork0.358 6917

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