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- PDB-6jqq: KatE H392C from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 6jqq
TitleKatE H392C from Escherichia coli
ComponentsCatalase
KeywordsOXIDOREDUCTASE / KatE / catalase / mutant
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding
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
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesEscherichia coli ISC7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPark, J.B. / Cho, H.-S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
Citation
Journal: To Be Published
Title: KatE H392C from Escherichia coli
Authors: Park, J.B. / Cho, H.-S.
#1: Journal: Structure / Year: 1995
Title: Crystal structure of catalase HPII from Escherichia coli.
Authors: Bravo, J. / Verdaguer, N. / Tormo, J. / Betzel, C. / Switala, J. / Loewen, P.C. / Fita, I.
History
DepositionApr 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,6949
Polymers337,1664
Non-polymers2,5285
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58930 Å2
ΔGint-285 kcal/mol
Surface area79070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.345, 129.099, 117.372
Angle α, β, γ (deg.)90.00, 109.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Catalase


Mass: 84291.531 Da / Num. of mol.: 4 / Mutation: H392C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli ISC7 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: W1F4G9, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 300 K / Method: vapor diffusion
Details: 0.2M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→45.16 Å / Num. obs: 91443 / % possible obs: 91.87 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.219 / Net I/σ(I): 2
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.397 / Num. unique obs: 4258

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IPH

1iph


Resolution: 2.4→45.16 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 16.307 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27907 4447 4.9 %RANDOM
Rwork0.24429 ---
obs0.24601 86374 91.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.152 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22909 0 176 343 23428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01323729
X-RAY DIFFRACTIONr_bond_other_d0.0020.01721511
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.66432319
X-RAY DIFFRACTIONr_angle_other_deg1.5561.58349968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69852891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55622.0831344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.386153757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.37315175
X-RAY DIFFRACTIONr_chiral_restr0.0750.23011
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226958
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025127
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1863.21111585
X-RAY DIFFRACTIONr_mcbond_other1.1863.21111584
X-RAY DIFFRACTIONr_mcangle_it1.9514.81314469
X-RAY DIFFRACTIONr_mcangle_other1.9514.81314470
X-RAY DIFFRACTIONr_scbond_it1.2023.2812144
X-RAY DIFFRACTIONr_scbond_other1.2023.2812145
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0244.8817851
X-RAY DIFFRACTIONr_long_range_B_refined4.20560.40699163
X-RAY DIFFRACTIONr_long_range_B_other4.20560.40599164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 263 -
Rwork0.373 5729 -
obs--82.19 %

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