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- PDB-3ttu: Structure of F413Y/H128N double variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 3ttu
TitleStructure of F413Y/H128N double variant of E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / heme orientation
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
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 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 / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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)339,5208
Polymers337,0544
Non-polymers2,4664
Water51,1632840
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58810 Å2
ΔGint-285 kcal/mol
Surface area79540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.620, 132.960, 122.670
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: 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: 84263.406 Da / Num. of mol.: 4 / Mutation: F413Y/H128N
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.: 2840 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.543 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 19, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.543 Å / Relative weight: 1
ReflectionResolution: 1.89→35.462 Å / Num. all: 223987 / Num. obs: 188835 / % possible obs: 84.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.062 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.89-23.60.2143.676557213700.21465.5
2-2.123.70.1654.691217246390.16579.7
2.12-2.263.80.1295.886771227120.12978.2
2.26-2.453.90.1076.6101796261020.10796.5
2.45-2.683.90.0878.184684215030.08786.4
2.68-340.05712.485019212070.05794.2
3-3.4640.04714.773187181580.04791.1
3.46-4.2440.04216.153193131890.04278.4
4.24-5.9940.03319.152480129760.03399.5
5.99-35.46240.02723.62862871820.02799.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GGE

1gge


Resolution: 1.89→35.462 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.1803 / WRfactor Rwork: 0.1364 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8917 / SU B: 6.01 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1727 / SU Rfree: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 9439 5 %RANDOM
Rwork0.1441 ---
all0.1466 188835 --
obs0.1466 188835 84.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.61 Å2 / Biso mean: 15.8522 Å2 / Biso min: 3.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å20.23 Å2
2--0.11 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.89→35.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22948 0 172 2840 25960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02223800
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.97932428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54152904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69923.8781176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.784153764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.55415176
X-RAY DIFFRACTIONr_chiral_restr0.1470.23416
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02118772
X-RAY DIFFRACTIONr_mcbond_it0.8971.514544
X-RAY DIFFRACTIONr_mcangle_it1.373223522
X-RAY DIFFRACTIONr_scbond_it2.37639256
X-RAY DIFFRACTIONr_scangle_it3.3724.58904
Refine LS restraints NCS

Ens-ID: 1 / Number: 5742 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.390.5
2BMEDIUM POSITIONAL0.350.5
3CMEDIUM POSITIONAL0.340.5
4DMEDIUM POSITIONAL0.350.5
1AMEDIUM THERMAL1.232
2BMEDIUM THERMAL1.12
3CMEDIUM THERMAL1.112
4DMEDIUM THERMAL1.052
LS refinement shellResolution: 1.89→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 522 -
Rwork0.178 10417 -
all-10939 -
obs--66.15 %
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)
10.379-0.0084-0.00790.24870.00720.3439-0.0045-0.0822-0.05250.07040.00960.03970.0472-0.0305-0.00520.026-0.00120.00920.02120.01450.03742.6598-9.319931.3484
20.3976-0.03930.03160.29170.02210.30280.00180.13010.052-0.12790.00020.0228-0.0416-0.0199-0.00210.0615-0.0015-0.01210.04660.02030.04823.707211.8428-18.4845
30.382-0.0151-0.07290.2998-0.04560.3217-0.00890.1192-0.0502-0.13270.0057-0.02130.06540.02280.00330.0653-0.00080.01020.0451-0.01640.03726.635-11.9092-19.4534
40.39970.04350.00720.2816-0.02330.33910.002-0.09590.04940.0814-0.0005-0.0282-0.05620.0548-0.00150.0316-0.0056-0.0060.0334-0.01210.024930.02879.264431.4702
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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