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- PDB-4enp: Structure of E530A variant E. coli KatE -

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Basic information

Entry
Database: PDB / ID: 4enp
TitleStructure of E530A variant E. coli KatE
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / E530A 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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 9, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: 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_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)339,3208
Polymers336,8544
Non-polymers2,4664
Water60,2423344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58210 Å2
ΔGint-288 kcal/mol
Surface area79690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.330, 133.110, 122.740
Angle α, β, γ (deg.)90.000, 109.410, 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: 84213.414 Da / Num. of mol.: 4 / Mutation: E530A
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3344 / 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: 42.38 %
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: 1.5→133.11 Å / Num. all: 449780 / Num. obs: 449780 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.079 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.583.60.2882.4238916656330.288100
1.58-1.683.70.2093.3229906620410.209100
1.68-1.793.80.1614.2218887583620.161100
1.79-1.943.80.134.9204818543190.13100
1.94-2.123.80.1025.9190593500280.102100
2.12-2.373.80.0896.5173119452080.089100
2.37-2.743.80.0896.5153433399840.089100
2.74-3.353.90.0688.7130684337970.068100
3.35-4.743.80.05211.5100611261520.05299.9
4.74-35.2453.70.04812.853429142560.04898.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementResolution: 1.5→35.24 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.1472 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9223 / SU B: 1.812 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0606 / SU Rfree: 0.0618 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.162 22572 5 %RANDOM
Rwork0.1376 427158 --
obs0.1388 449730 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.96 Å2 / Biso mean: 17.5621 Å2 / Biso min: 5.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.5 Å2
2---0.17 Å2-0 Å2
3---0.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.036 Å
Refinement stepCycle: LAST / Resolution: 1.5→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22936 0 172 3344 26452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224055
X-RAY DIFFRACTIONr_angle_refined_deg2.651.96632810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37252956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60623.8451186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.587153829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2915179
X-RAY DIFFRACTIONr_chiral_restr0.1870.23460
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02119015
Refine LS restraints NCS

Ens-ID: 1 / Number: 5705 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.310.5
2BMEDIUM POSITIONAL0.310.5
3CMEDIUM POSITIONAL0.30.5
4DMEDIUM POSITIONAL0.30.5
1AMEDIUM THERMAL3.72
2BMEDIUM THERMAL3.422
3CMEDIUM THERMAL2.92
4DMEDIUM THERMAL2.632
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 1680 -
Rwork0.193 31153 -
all-32833 -
obs--99.94 %
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)
10.0694-0.01250.00720.0426-0.01060.0505-0.013-0.0241-0.02750.00690.01490.02030.0001-0.0009-0.00190.00540.00650.01170.01160.01510.02632.4504-9.221431.7931
20.069-0.0117-0.00640.0696-0.00980.04280.00090.02570.0186-0.03010.00250.0137-0.0077-0.0011-0.00340.0175-0.0036-0.00850.0120.01190.01663.332411.8309-19.1013
30.08580.018-0.01230.0549-0.00930.0566-0.01250.0283-0.0119-0.02840.0097-0.00430.01750.00670.00270.0241-0.00450.01170.0123-0.00530.013826.161-11.8233-19.6649
40.0830.0336-0.01420.03970.00160.0430.0042-0.02690.00980.005-0.0026-0.0023-0.00890.0176-0.00160.0035-0.00180.00190.0169-0.00220.015629.57689.172631.1869
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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