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- PDB-4enw: Structure of the S234N variant of E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 4enw
TitleStructure of the S234N variant of E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase fold / KatE / S234N variant
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 / cytoplasm / cytosol
Similarity search - Function
Catalase, four-helical domain / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / 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 / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / 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
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLoewen, P.C. / Jha, V.
CitationJournal: Arch.Biochem.Biophys. / Year: 2012
Title: Influence of main channel structure on H(2)O(2) access to the heme cavity of catalase KatE of Escherichia coli.
Authors: Jha, V. / Chelikani, P. / Carpena, X. / Fita, I. / Loewen, P.C.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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)339,7248
Polymers337,1944
Non-polymers2,5304
Water49,5772752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58830 Å2
ΔGint-277 kcal/mol
Surface area78160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.393, 132.570, 122.567
Angle α, β, γ (deg.)90.000, 109.230, 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: 84298.477 Da / Num. of mol.: 4 / Mutation: S234N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2752 / 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: 42.11 %
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: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011 / Details: mirrors
RadiationMonochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→35.131 Å / Num. all: 206796 / Num. obs: 206796 / % possible obs: 93.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.086 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-22.70.2382.175231274960.23885.5
2-2.1230.1434.485526284150.14393.1
2.12-2.272.90.165374230256350.16589.7
2.27-2.453.30.1225.385032259490.12297.1
2.45-2.693.30.1095.976356231190.10994.5
2.69-33.50.0768.277829221450.07699.4
3-3.473.50.0659.465653189700.06596.8
3.47-4.253.30.0611050866153220.06192.2
4.25-6.013.60.0571046148128670.057100
6.01-35.1313.40.04313.92359768780.04396.4

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Processing

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

1gge


Resolution: 1.9→35.131 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2299 / WRfactor Rwork: 0.1802 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8612 / SU B: 5.9 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1828 / SU Rfree: 0.1589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 10355 5 %RANDOM
Rwork0.1746 ---
obs0.1769 206533 93.41 %-
all-206796 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.26 Å2 / Biso mean: 15.5443 Å2 / Biso min: 2.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.46 Å2
2---0.26 Å20 Å2
3---0.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.092 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22960 0 176 2752 25888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223841
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.96732505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56852912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75723.871181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.966153768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.16115176
X-RAY DIFFRACTIONr_chiral_restr0.1510.23427
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02118836
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5736 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.310.5
BMEDIUM POSITIONAL0.310.5
CMEDIUM POSITIONAL0.320.5
DMEDIUM POSITIONAL0.350.5
AMEDIUM THERMAL2.272
BMEDIUM THERMAL2.062
CMEDIUM THERMAL1.992
DMEDIUM THERMAL1.812
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 662 -
Rwork0.409 12674 -
all-13336 -
obs--82.66 %
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)
10.05750.00050.02460.0814-0.01860.0459-0.0056-0.015-0.02450.02250.01210.02470.0012-0.01-0.00650.010.00350.01080.00960.01090.02352.5142-9.191131.7428
20.0656-0.0355-0.02570.1033-0.01130.05130.00550.01360.0229-0.0474-0.00270.00930.0004-0.0123-0.00290.02720.0001-0.01370.00870.00790.02183.452111.7914-18.8396
30.061-0.00710.00310.0942-0.0030.0552-0.00910.0101-0.0241-0.050.0044-0.010.01170.0110.00470.0335-0.00570.01510.0092-0.00910.017626.1321-11.6795-19.4655
40.080.0412-0.02320.08650.0050.03570.0106-0.01810.01350.0226-0.0031-0.0057-0.00780.0216-0.00750.0111-0.0032-0.00380.019-0.00910.014529.60279.043231.1587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 753
2X-RAY DIFFRACTION1A801
3X-RAY DIFFRACTION2B28 - 753
4X-RAY DIFFRACTION2B801
5X-RAY DIFFRACTION3C28 - 753
6X-RAY DIFFRACTION3C801
7X-RAY DIFFRACTION4D28 - 753
8X-RAY DIFFRACTION4D801

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