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- PDB-3p9q: Structure of I274C variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 3p9q
TitleStructure of I274C variant of E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / I274C 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 / 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
HYDROSULFURIC ACID / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Chem-HDE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLoewen, P.C. / Jha, V. / Louis, S. / Chelikani, P. / Carpena, X. / Fita, I.
CitationJournal: Biochemistry / Year: 2011
Title: Modulation of heme orientation and binding by a single residue in catalase HPII of Escherichia coli.
Authors: Jha, V. / Louis, S. / Chelikani, P. / Carpena, X. / Donald, L.J. / Fita, I. / Loewen, P.C.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: 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_conn_type / 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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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)342,01016
Polymers336,7894
Non-polymers5,22012
Water62,9803496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57570 Å2
ΔGint-299 kcal/mol
Surface area79370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.660, 133.020, 122.590
Angle α, β, γ (deg.)90.00, 109.59, 90.00
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: 84197.305 Da / Num. of mol.: 4 / Mutation: I274C
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-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-HDE / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 17R, 18S


Mass: 638.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H38FeN4O5
#4: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3496 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
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: 0.97934 Å
DetectorType: Marmosaic / Detector: CCD / Date: Dec 9, 2009 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.48→28.55 Å / Num. all: 429958 / Num. obs: 429958 / % possible obs: 91.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rsym value: 0.081 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.48-1.562.70.4831.6148179544120.48379.7
1.56-1.652.70.3442.2148691542000.34483.9
1.65-1.772.80.2393.1148959535410.23988.2
1.77-1.912.80.1674.4149016524350.16792.7
1.91-2.0930.1215.8149946501940.12196.6
2.09-2.343.30.0917.6151677464830.09198.6
2.34-2.73.50.0778.8146345413150.07799.4
2.7-3.313.80.078.8132955351150.0799.8
3.31-4.683.90.05112.4105195272550.051100
4.68-28.5533.80.0371657311150080.03799.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→28.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.1408 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9085 / SU B: 2.518 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0664 / SU Rfree: 0.0706 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 21507 5 %RANDOM
Rwork0.1434 ---
all0.1451 429958 --
obs0.1451 429789 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.11 Å2 / Biso mean: 14.4252 Å2 / Biso min: 2.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20.4 Å2
2---0.48 Å2-0 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.48→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22936 0 356 3496 26788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02224090
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.98932914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41652908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80123.8381183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83153782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.01615178
X-RAY DIFFRACTIONr_chiral_restr0.2260.23447
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02118986
X-RAY DIFFRACTIONr_mcbond_it1.2391.514571
X-RAY DIFFRACTIONr_mcangle_it1.921223577
X-RAY DIFFRACTIONr_scbond_it2.83839519
X-RAY DIFFRACTIONr_scangle_it4.234.59337
Refine LS restraints NCS

Ens-ID: 1 / Number: 5699 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.370.5
2BMEDIUM POSITIONAL0.320.5
3CMEDIUM POSITIONAL0.310.5
4DMEDIUM POSITIONAL0.340.5
1AMEDIUM THERMAL1.862
2BMEDIUM THERMAL1.622
3CMEDIUM THERMAL1.522
4DMEDIUM THERMAL1.412
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 1321 -
Rwork0.264 25943 -
all-27264 -
obs--78.78 %
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)
10.0929-0.00430.01150.1072-0.01340.0741-0.009-0.0232-0.03070.02210.01330.03080.0081-0.006-0.00430.00880.00360.00850.01040.01350.02052.6378-9.316431.507
20.082-0.0255-0.0180.1425-0.01180.07970.00240.02360.0296-0.06750.00290.0168-0.0099-0.008-0.00520.0379-0.005-0.01380.01120.01270.01743.665411.8338-18.5991
30.08740.01140.00250.131-0.00910.0731-0.01290.0202-0.0204-0.07220.0097-0.01630.02740.01670.00330.0486-0.00320.01280.0112-0.00680.008126.5891-12.0283-19.628
40.10070.029-0.0220.1024-0.00020.05810.0028-0.03050.01680.023-0.0009-0.0144-0.01270.0262-0.00190.0102-0.0015-0.00510.0205-0.00620.007630.07499.441831.518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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