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- PDB-3pq5: Structure of I274C variant of E. coli KatE[] - Images 19-24 -

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Basic information

Entry
Database: PDB / ID: 3pq5
TitleStructure of I274C variant of E. coli KatE[] - Images 19-24
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / I274C variant / heme orientation / X-ray damage
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
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: 1.8 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
DepositionNov 25, 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 1.4Sep 6, 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_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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water62,0263443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57640 Å2
ΔGint-299 kcal/mol
Surface area79430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.503, 133.022, 122.674
Angle α, β, γ (deg.)90.000, 109.400, 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 / 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.: 3443 / 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: 33

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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 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: Aug 27, 2009 / Details: mirrors
RadiationMonochromator: Double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.795→31.962 Å / Num. all: 244091 / Num. obs: 244091 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.148 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.92.80.371.694335336990.3788.5
1.9-2.012.90.2892.195356328340.28991.1
2.01-2.1530.2212.993643312540.22192.3
2.15-2.323.10.2142.791201295100.21493.5
2.32-2.553.20.191287871274530.19194.5
2.55-2.853.30.163.283144250440.1695.4
2.85-3.293.50.1344.677520223330.13496.3
3.29-4.023.60.1244.768783190090.12496.7
4.02-5.693.70.0966.254979148230.09697.5
5.69-32.1513.70.0727.72974681320.07296.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3P9Q

3p9q


Resolution: 1.8→31.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.1926 / WRfactor Rwork: 0.1459 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9062 / SU B: 5.073 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1246 / SU Rfree: 0.1212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 12210 5 %RANDOM
Rwork0.1432 ---
obs0.1455 243857 92.69 %-
all-244091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.23 Å2 / Biso mean: 14.0953 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20.37 Å2
2---0.35 Å2-0 Å2
3---0.78 Å2
Refine analyzeLuzzati coordinate error obs: 0.071 Å
Refinement stepCycle: LAST / Resolution: 1.8→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22936 0 356 3443 26735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02224102
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.98932898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50152908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59623.8531181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.152153780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.83615177
X-RAY DIFFRACTIONr_chiral_restr0.1810.23447
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02118973
X-RAY DIFFRACTIONr_mcbond_it1.1131.514579
X-RAY DIFFRACTIONr_mcangle_it1.684223575
X-RAY DIFFRACTIONr_scbond_it2.71839523
X-RAY DIFFRACTIONr_scangle_it3.9524.59323
Refine LS restraints NCS

Ens-ID: 1 / Number: 5705 / 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 POSITIONAL0.330.5
1AMEDIUM THERMAL2.022
2BMEDIUM THERMAL1.822
3CMEDIUM THERMAL1.682
4DMEDIUM THERMAL1.622
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 776 -
Rwork0.219 14811 -
all-15587 -
obs-14811 80.63 %
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)
10.05210.00460.01730.0624-0.01710.0339-0.0061-0.015-0.0250.01210.01210.021-0.0013-0.0039-0.00610.00730.00460.00890.01250.01410.02462.6635-9.308231.5439
20.044-0.0258-0.02180.0853-0.01530.03790.0060.00760.0205-0.04180.00530.010.001-0.0064-0.01130.0297-0.0051-0.01460.00910.01070.02223.609611.8383-18.5949
30.03630.0173-0.00650.0813-0.00330.0461-0.0126-0.0004-0.0066-0.04820.0122-0.00820.01890.01120.00040.0395-0.00540.01110.0082-0.00520.010126.4993-12.0076-19.6443
40.0670.0323-0.02570.06320.00670.03160.0074-0.01810.01040.0129-0.0027-0.0083-0.00710.0191-0.00470.0102-0.0009-0.00440.023-0.00350.011330.06799.423231.57
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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