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- PDB-3ttt: Structure of F413Y variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 3ttt
TitleStructure of F413Y 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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)339,6168
Polymers337,1504
Non-polymers2,4664
Water54,1893008
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58760 Å2
ΔGint-275 kcal/mol
Surface area79840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.560, 133.330, 122.160
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 / Catalase KatE / Hydroxyperoxidase II


Mass: 84287.453 Da / Num. of mol.: 4 / Mutation: F413Y
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.: 3008 / 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: 42.23 %
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: Feb 7, 2010 / 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: 1.58→29.232 Å / Num. all: 381546 / Num. obs: 376838 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.121 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.58-1.674.10.5641.2223239547920.56498.6
1.67-1.774.10.3721.9211723520140.37298.8
1.77-1.894.10.2832.2196459485010.28398.2
1.89-2.044.20.1624.3188454451490.16298.2
2.04-2.244.30.1295.3179837417620.12998.6
2.24-2.54.40.1254.8168357380620.12599.2
2.5-2.894.60.1095.8155443337660.10999.7
2.89-3.544.80.0936.8137880286340.09399.9
3.54-5.014.90.0758.2108593221900.07599.9
5.01-29.2324.70.079756262120690.07998.2

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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: 1.58→29.232 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1946 / WRfactor Rwork: 0.1618 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.885 / SU B: 3.113 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0817 / SU Rfree: 0.0825 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 18949 5 %RANDOM
Rwork0.157 ---
all0.1586 376838 --
obs0.1586 376838 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.39 Å2 / Biso mean: 16.5443 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.46 Å2
2---0.38 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.58→29.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22956 0 172 3008 26136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223812
X-RAY DIFFRACTIONr_angle_refined_deg2.51.96632444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31852904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63123.8441176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.021153764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.12515176
X-RAY DIFFRACTIONr_chiral_restr0.1940.23416
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02118788
Refine LS restraints NCS

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

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.410.5
BMEDIUM POSITIONAL0.360.5
CMEDIUM POSITIONAL0.350.5
DMEDIUM POSITIONAL0.360.5
AMEDIUM THERMAL3.362
BMEDIUM THERMAL2.662
CMEDIUM THERMAL2.472
DMEDIUM THERMAL2.352
LS refinement shellResolution: 1.58→1.625 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 1377 -
Rwork0.251 26018 -
all-27395 -
obs--98.48 %
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)
10.05530.00420.0110.0548-0.01060.0525-0.0072-0.0162-0.02070.0140.01410.02820.0042-0.0075-0.00690.00710.00640.01050.01260.01250.02562.5-9.163931.7441
20.0662-0.0294-0.01460.0952-0.00680.0487-0.00040.02190.0262-0.05030.01030.02-0.0074-0.0114-0.00990.0366-0.0111-0.01980.01330.01680.02283.387111.7699-19.1098
30.06150.00870.00140.0913-0.01240.0608-0.01770.0158-0.0187-0.05630.0178-0.01570.02190.0151-00.0412-0.010.01350.0122-0.00840.009226.1686-11.8725-19.6249
40.06780.0458-0.01460.0537-0.00270.05160.0071-0.01780.01150.0138-0.0031-0.0091-0.01340.0239-0.0040.0101-0.001-0.00440.0213-0.00330.018629.66899.213531.0809
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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