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- PDB-4ens: Structure of E530Q variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 4ens
TitleStructure of E530Q variant of E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / E530Q variant / heme orientation
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 / cytosol / cytoplasm
Similarity search - Function
Catalase, four-helical domain / 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 / 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 / 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 / Hemocyanin, N-terminal domain / 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 / 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
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLoewen, P.C. / Jha, V.
CitationJournal: Arch.Biochem.Biophys. / Year: 2012
Title: Influence of main channel structure on H(2)O(2) access to the heme cavity of catalase KatE of Escherichia coli.
Authors: Jha, V. / Chelikani, P. / Carpena, X. / Fita, I. / Loewen, P.C.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Feb 28, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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 HPII
B: Catalase HPII
C: Catalase HPII
D: Catalase HPII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,07812
Polymers337,0824
Non-polymers4,9968
Water53,1082948
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62150 Å2
ΔGint-348 kcal/mol
Surface area79400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.450, 133.400, 123.240
Angle α, β, γ (deg.)90.000, 109.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 28 - 753 / Label seq-ID: 28 - 753

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Catalase HPII / Hydroxyperoxidase II


Mass: 84270.461 Da / Num. of mol.: 4 / Mutation: E530Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1732, JW1721, katE / Plasmid: pKS / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P21179, catalase
#2: Chemical
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME / Heme


Mass: 632.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O5
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2948 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 17% PEG3350, 1.6 M LiCl, 0.1 M Tris, pH 9.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011 / Details: mirrors
RadiationMonochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→116.399 Å / Num. all: 344208 / Num. obs: 344208 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.099 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.692.70.3512.1111829421560.35177.6
1.69-1.792.60.2662.5112529427490.26683.1
1.79-1.912.70.2113.3115737431730.21189.3
1.91-2.072.90.1544.3123443429530.15495.2
2.07-2.263.20.1374.6130890409550.13798.7
2.26-2.533.60.1235133502375090.12399.5
2.53-2.923.80.1016.1125058330930.10199.8
2.92-3.583.80.0887107251280400.08899.9
3.58-5.063.80.0689.283092217840.06899.9
5.06-32.193.70.05910.244110117960.05998

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→32.19 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1931 / WRfactor Rwork: 0.1579 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9049 / SU B: 2.763 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0872 / SU Rfree: 0.0876 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 17269 5 %RANDOM
Rwork0.1509 ---
all0.1525 344208 --
obs0.1525 343592 91.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.99 Å2 / Biso mean: 16.28 Å2 / Biso min: 3.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.09 Å2
2--0.13 Å20 Å2
3---0.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.051 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22952 0 348 2948 26248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224078
X-RAY DIFFRACTIONr_angle_refined_deg2.5691.97732897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49252930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51223.8541178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.143153781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3615176
X-RAY DIFFRACTIONr_chiral_restr0.190.23439
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02119044
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5708 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.30.5
BMEDIUM POSITIONAL0.310.5
CMEDIUM POSITIONAL0.330.5
DMEDIUM POSITIONAL0.340.5
AMEDIUM THERMAL2.752
BMEDIUM THERMAL2.212
CMEDIUM THERMAL2.032
DMEDIUM THERMAL1.852
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 990 -
Rwork0.204 19860 -
all-20850 -
obs-42156 75.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05460.01750.01020.0509-0.00890.0432-0.0028-0.0165-0.01590.00930.00660.01360.0046-0.0051-0.00390.00540.00370.00560.01440.00760.01362.456-9.277131.8682
20.0379-0.0306-0.02160.0943-0.00810.03340.00910.0080.0102-0.0411-0.00240.0116-0.0029-0.0048-0.00670.0274-0.0009-0.01260.0070.00560.01253.413911.9045-18.9422
30.0429-0.0090.01380.0776-0.00210.0409-0.00440.0069-0.0145-0.04190.0062-0.00640.0130.011-0.00180.0316-0.00380.00970.0108-0.00750.009926.1323-11.7351-19.5946
40.07420.053-0.02120.05750.00170.03740.0121-0.02280.01340.0097-0.0053-0.0023-0.00640.0188-0.00680.0035-0.0017-0.00060.0215-0.01080.012929.61759.083331.3059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 753
2X-RAY DIFFRACTION1A801 - 802
3X-RAY DIFFRACTION2B28 - 753
4X-RAY DIFFRACTION2B801 - 802
5X-RAY DIFFRACTION3C28 - 753
6X-RAY DIFFRACTION3C801 - 802
7X-RAY DIFFRACTION4D28 - 753
8X-RAY DIFFRACTION4D801 - 802

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