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- PDB-3ttx: Structure of the F413K variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 3ttx
TitleStructure of the F413K variant of E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / 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 / 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 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
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLoewen, P.C. / Jha, V.
CitationJournal: Arch.Biochem.Biophys. / Year: 2012
Title: Mutation of Phe413 to Tyr in catalase KatE from Escherichia coli leads to side chain damage and main chain cleavage.
Authors: Jha, V. / Donald, L.J. / Loewen, P.C.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)339,6728
Polymers337,2064
Non-polymers2,4664
Water51,4512856
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58620 Å2
ΔGint-284 kcal/mol
Surface area79190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 132.960, 122.030
Angle α, β, γ (deg.)90.000, 109.690, 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 / Catalase KatE / Hydroxyperoxidase II


Mass: 84301.453 Da / Num. of mol.: 4 / Mutation: F413K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b1732, JW1721, katE / Plasmid: pKS / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / 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.: 2856 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 17% PEG3350, 1.6 M lithium chloride, 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: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2009 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.74→35.182 Å / Num. all: 286682 / Num. obs: 278239 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.106 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.74-1.833.30.4581.6125281374230.45889.8
1.83-1.953.60.3272.2135975380710.32796.5
1.95-2.083.60.2263.3131036361600.22697.5
2.08-2.253.70.1584.6124472338890.15898.3
2.25-2.463.70.1274117679315010.12798.8
2.46-2.753.80.0977.5108263285700.09799.2
2.75-3.183.90.0749.497694252680.07499.5
3.18-3.893.90.0659.483893215060.06599.7
3.89-5.53.90.069.664939166840.0699.9
5.5-35.1823.80.05111.33539192020.05199.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GGE

1gge


Resolution: 1.74→35.182 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.1772 / WRfactor Rwork: 0.14 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9133 / SU B: 4.351 / SU ML: 0.063 / SU R Cruickshank DPI: 0.105 / 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 ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 14075 5.1 %RANDOM
Rwork0.1457 ---
all0.1477 278239 --
obs0.1477 278239 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.95 Å2 / Biso mean: 14.151 Å2 / Biso min: 2.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20.41 Å2
2---0.09 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.74→35.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22956 0 172 2856 25984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02223808
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.97932440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4352904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13823.8571172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.335153780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9915176
X-RAY DIFFRACTIONr_chiral_restr0.1860.23416
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02118748
X-RAY DIFFRACTIONr_mcbond_it1.151.514544
X-RAY DIFFRACTIONr_mcangle_it1.842223522
X-RAY DIFFRACTIONr_scbond_it2.87939264
X-RAY DIFFRACTIONr_scangle_it4.3954.58916
Refine LS restraints NCS

Ens-ID: 1 / Number: 5744 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.390.5
2BMEDIUM POSITIONAL0.350.5
3CMEDIUM POSITIONAL0.350.5
4DMEDIUM POSITIONAL0.350.5
1AMEDIUM THERMAL1.912
2BMEDIUM THERMAL1.712
3CMEDIUM THERMAL1.722
4DMEDIUM THERMAL1.592
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 908 -
Rwork0.252 16895 -
all-17803 -
obs--84 %
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)
10.0397-0.00230.01330.0297-0.01780.036-0.0071-0.0073-0.01440.0010.00940.0150.0019-0.0049-0.00230.0030.00230.00420.00720.00630.01932.7485-9.228631.2505
20.08050.00120.00180.0851-00.0464-0.00820.0240.0163-0.03890.00990.0148-0.0104-0.0013-0.00170.0233-0.0078-0.01130.01220.01070.01213.673411.7531-18.665
30.08180.0316-0.01890.0791-0.01670.0597-0.01960.0208-0.0081-0.03890.0156-0.00990.01880.00290.0040.0222-0.00770.00680.0109-0.00640.00626.5566-12.0166-19.5572
40.04850.0304-0.01880.03720.01020.04190.0044-0.01150.00750.0015-0.0025-0.002-0.00620.0147-0.00190.0025-0.001-0.00330.013-0.00070.01529.9419.402631.29
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 753
2X-RAY DIFFRACTION2B28 - 753
3X-RAY DIFFRACTION3C28 - 753
4X-RAY DIFFRACTION4D28 - 753

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