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- PDB-4env: Structure of the S234I variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 4env
TitleStructure of the S234I variant of E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase fold / KatE / S234D variant
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
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: 1.7 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 1.2Sep 13, 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 / 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)342,18612
Polymers337,1904
Non-polymers4,9968
Water54,0633001
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62040 Å2
ΔGint-348 kcal/mol
Surface area78610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.230, 133.130, 122.710
Angle α, β, γ (deg.)90.000, 109.390, 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: LEU / Beg label comp-ID: LEU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 29 - 753 / Label seq-ID: 29 - 753

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

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Components

#1: Protein
Catalase HPII / Hydroxyperoxidase II


Mass: 84297.531 Da / Num. of mol.: 4 / Mutation: S234I
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.: 3001 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
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→32.122 Å / Num. all: 246545 / Num. obs: 246545 / % possible obs: 79.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rsym value: 0.062 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.791.80.1883.752942293050.18865.3
1.79-1.91.80.173449266279370.17365.8
1.9-2.031.80.1762.849399279050.17670
2.03-2.191.80.0986.451931288360.09877.5
2.19-2.41.80.1273.552987290690.12784.9
2.4-2.6920.0768.458767291080.07693.7
2.69-3.12.30.05311.861798264510.05396.3
3.1-3.82.70.0551059099221970.05595.6
3.8-5.382.90.0415.348417168870.0493.9
5.38-32.1222.90.03120.52610388500.03188.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GGE

1gge


Resolution: 1.7→32.122 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2148 / WRfactor Rwork: 0.1729 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8628 / SU B: 3.797 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1417 / SU Rfree: 0.1298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 12422 5.1 %RANDOM
Rwork0.1672 ---
obs0.1692 245687 79.47 %-
all-246545 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.85 Å2 / Biso mean: 15.8515 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å20.08 Å2
2--0.56 Å2-0 Å2
3---0.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.068 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22960 0 348 3001 26309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224029
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.97732810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54252904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37523.8711178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54153774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3715176
X-RAY DIFFRACTIONr_chiral_restr0.1690.23429
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02118988
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5730 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.360.5
BMEDIUM POSITIONAL0.310.5
CMEDIUM POSITIONAL0.320.5
DMEDIUM POSITIONAL0.320.5
AMEDIUM THERMAL2.662
BMEDIUM THERMAL2.192
CMEDIUM THERMAL2.522
DMEDIUM THERMAL2.122
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 758 -
Rwork0.193 14048 -
all-14806 -
obs--64.97 %
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)
10.0698-0.00120.01850.0672-0.02360.0415-0.0073-0.0199-0.02980.01110.01550.0262-0.0033-0.0021-0.00810.00370.00510.0080.01150.01670.02512.457-9.219731.7825
20.075-0.0465-0.02790.0948-0.01170.03740.01430.02070.0231-0.0407-0.00510.01330.0007-0.0045-0.00920.023-0.0034-0.01560.00940.01450.02763.360611.8294-18.9337
30.0607-0.0170.0060.0977-0.00630.0391-0.00090.0122-0.015-0.0533-0.0038-0.00890.0190.0060.00470.03820.00090.01090.0098-0.00650.008926.1012-11.7115-19.5545
40.09170.0489-0.02620.0555-0.00680.0370.0093-0.02640.0170.0094-0.0065-0.001-0.00780.0243-0.00290.0053-0.0018-0.00260.0224-0.00740.008929.55939.075531.2046
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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