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- PDB-6by0: Crystal structure of catalase HPII from E. coli in space group P1 -

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Basic information

Entry
Database: PDB / ID: 6by0
TitleCrystal structure of catalase HPII from E. coli in space group P1
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase HPII
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 / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsLisa, M.N. / Buschiazzo, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: SIMBAD: a sequence-independent molecular-replacement pipeline.
Authors: Simpkin, A.J. / Simkovic, F. / Thomas, J.M.H. / Savko, M. / Lebedev, A. / Uski, V. / Ballard, C. / Wojdyr, M. / Wu, R. / Sanishvili, R. / Xu, Y. / Lisa, M.N. / Buschiazzo, A. / Shepard, W. / ...Authors: Simpkin, A.J. / Simkovic, F. / Thomas, J.M.H. / Savko, M. / Lebedev, A. / Uski, V. / Ballard, C. / Wojdyr, M. / Wu, R. / Sanishvili, R. / Xu, Y. / Lisa, M.N. / Buschiazzo, A. / Shepard, W. / Rigden, D.J. / Keegan, R.M.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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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)339,5528
Polymers337,0864
Non-polymers2,4664
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58850 Å2
ΔGint-291 kcal/mol
Surface area77960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.337, 90.141, 114.764
Angle α, β, γ (deg.)107.10, 105.60, 95.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Catalase HPII / Hydroxyperoxidase II


Mass: 84271.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / 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.: 603 / 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: 1.92 Å3/Da / Density % sol: 35.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.085 M sodium HEPES pH 7.5, 17% w/v PEG 4000, 15% v/v glycerol, 8.5% v/v isopropanol or 0.1 M HEPES pH 7.0, 20% w/v PEG 6000, 1.0 M lithium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.93→49.39 Å / Num. obs: 53296 / % possible obs: 98.8 % / Redundancy: 6 % / Biso Wilson estimate: 34.55 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.174 / Net I/σ(I): 4.3
Reflection shellResolution: 2.93→3.02 Å / Rmerge(I) obs: 0.506 / Num. unique obs: 4616

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
AMoRESIMBADphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VU3

3vu3


Resolution: 2.93→49.39 Å / Cor.coef. Fo:Fc: 0.8419 / Cor.coef. Fo:Fc free: 0.7884 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.445
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 2598 4.9 %RANDOM
Rwork0.1831 ---
obs0.1857 53064 98.52 %-
Displacement parametersBiso mean: 24.29 Å2
Baniso -1Baniso -2Baniso -3
1--19.9215 Å22.616 Å2-4.6571 Å2
2--24.2731 Å27.1383 Å2
3----4.3516 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: 1 / Resolution: 2.93→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22894 0 172 603 23669
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123720HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0432304HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7986SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes628HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3493HARMONIC5
X-RAY DIFFRACTIONt_it23720HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion16.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3009SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28155SEMIHARMONIC4
LS refinement shellResolution: 2.93→3.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 193 4.9 %
Rwork0.2396 3747 -
all0.2448 3940 -
obs--97.89 %
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)
10.0151-0.05930.06490.0918-0.01460.2337-0.0466-0.0258-0.00390.0165-0.04570.0048-0.0934-0.06940.09230.07340.0044-0.0307-0.09180.01790.010359.242222.04911.5316
20.0549-0.14320.05730.26080.12920.3301-0.02990.0403-0.00120.07910.0506-0.02620.02940.0859-0.0206-0.0101-0.0254-0.0284-0.03410.0537-0.004282.9311-0.402110.2719
3-0.09070.01080.09160.3724-0.05710.2754-0.0256-0.05040.0233-0.0918-0.01530.03990.0553-0.01040.04090.0132-0.019-0.025-0.07760.02490.028152.7616-10.3045-34.2931
4-0.03130.13460.04670.3547-0.01360.2211-0.0136-0.00860.0196-0.11230.0078-0.0056-0.06050.0570.00580.0829-0.01570.0133-0.09920.0539-0.018270.016516.31-42.1425
50.5498-0.05110.17480.1036-0.1476-0.05240.0046-0.0043-0.00350.0002-0.0066-0.0025-0.00190.00150.002-0.00120-0.0039-0.00680.00550.001866.25516.918-13.6825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|28 - A|753 }A28 - 753
2X-RAY DIFFRACTION2{ B|29 - B|753 }B29 - 753
3X-RAY DIFFRACTION3{ C|28 - C|753 }C28 - 753
4X-RAY DIFFRACTION4{ D|28 - D|753 }D28 - 753
5X-RAY DIFFRACTION5{ A|801 - A|801 C|801 - C|801 B|801 - B|801 D|801 - D|801 }A801
6X-RAY DIFFRACTION5{ A|801 - A|801 C|801 - C|801 B|801 - B|801 D|801 - D|801 }C801
7X-RAY DIFFRACTION5{ A|801 - A|801 C|801 - C|801 B|801 - B|801 D|801 - D|801 }B801
8X-RAY DIFFRACTION5{ A|801 - A|801 C|801 - C|801 B|801 - B|801 D|801 - D|801 }D801

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