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- PDB-4ent: Structure of the S234A variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 4ent
TitleStructure of the S234A variant of E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / S234A 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 / 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
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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)342,21012
Polymers337,2144
Non-polymers4,9968
Water53,4512967
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62210 Å2
ΔGint-348 kcal/mol
Surface area79010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.460, 133.050, 122.190
Angle α, β, γ (deg.)90.000, 109.580, 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: 84303.445 Da / Num. of mol.: 4 / Mutation: S234A
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


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


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


Mass: 18.015 Da / Num. of mol.: 2967 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.05 %
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: 1.7→33.262 Å / Num. all: 302611 / Num. obs: 302611 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rsym value: 0.11 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.20.5541.2134632418940.55493.5
1.79-1.93.20.3951.7131830411120.39596.7
1.9-2.033.30.2452.8129410395050.24598.8
2.03-2.193.40.1763.9124216369320.17699.5
2.19-2.43.40.1484.6116753341140.14899.6
2.4-2.693.40.1424.5105517308930.14299.7
2.69-3.13.40.088.494129273160.0899.8
3.1-3.83.50.05711.479772231150.05799.9
3.8-5.383.50.0415.261823179000.0499.9
5.38-33.2623.40.03815.63376398300.03898.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementResolution: 1.7→33.262 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1519 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8886 / SU B: 3.883 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1048 / SU Rfree: 0.1038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 15289 5.1 %RANDOM
Rwork0.1583 287023 --
obs0.1603 302312 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.97 Å2 / Biso mean: 15.1685 Å2 / Biso min: 3.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20.46 Å2
2---0.18 Å20 Å2
3---0.81 Å2
Refine analyzeLuzzati coordinate error obs: 0.066 Å
Refinement stepCycle: LAST / Resolution: 1.7→33.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22960 0 348 2967 26275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224037
X-RAY DIFFRACTIONr_angle_refined_deg2.4451.97932834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27652912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17223.8551175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.487153763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.27715176
X-RAY DIFFRACTIONr_chiral_restr0.1840.23431
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02118996
Refine LS restraints NCS

Ens-ID: 1 / Number: 5713 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.330.5
2BMEDIUM POSITIONAL0.330.5
3CMEDIUM POSITIONAL0.320.5
4DMEDIUM POSITIONAL0.320.5
1AMEDIUM THERMAL2.682
2BMEDIUM THERMAL2.512
3CMEDIUM THERMAL2.332
4DMEDIUM THERMAL2.112
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 1017 -
Rwork0.239 19764 -
all-20781 -
obs--92.61 %
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)
10.0618-0.00790.01450.0409-0.01420.0451-0.0107-0.0165-0.02270.0080.01310.02430.0007-0.0005-0.00240.00420.00530.00910.0090.01340.02242.4792-9.148431.7419
20.0525-0.0283-0.01420.0751-0.01210.04540.00140.01410.0182-0.03240.00240.013-0.0042-0.0033-0.00390.0228-0.0059-0.01480.00770.01070.01773.423711.754-19.0735
30.05280.00640.00740.0664-0.00580.0423-0.01190.0105-0.0137-0.03650.0086-0.00310.01180.01190.00330.026-0.00460.00730.0088-0.00410.007426.1263-11.8458-19.5802
40.0690.0428-0.01690.04410.00580.03840.0053-0.01780.00870.0057-0.0042-0.0016-0.00680.0162-0.0010.0062-0.0001-0.00020.0146-0.00040.011729.59319.189431.1099
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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