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- PDB-6ztv: Crystal Structure of catalase HPII from Escherichia coli (serendi... -

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Basic information

Entry
Database: PDB / ID: 6ztv
TitleCrystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)
ComponentsCatalase HPII
KeywordsOXIDOREDUCTASE / catalase / hydrogen-peroxide / heme / iron / oxidative stress / artifact crystallization / impurities / contaminations
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
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 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive 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 / 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-like
Similarity search - Domain/homology
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGrzechowiak, M. / Sekula, B. / Ruszkowski, M.
Funding support Poland, United States, 3items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
Polish National Science CentreSYMFONIA 2016/20/W/ST5/00478 Poland
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Acta Biochim.Pol. / Year: 2021
Title: Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told".
Authors: Grzechowiak, M. / Sekula, B. / Jaskolski, M. / Ruszkowski, M.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 3, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 31, 2024Group: 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

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)340,07010
Polymers337,3864
Non-polymers2,6846
Water37,4172077
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59320 Å2
ΔGint-274 kcal/mol
Surface area79850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.784, 172.257, 123.176
Angle α, β, γ (deg.)90.000, 104.517, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Catalase HPII / Hydroxyperoxidase II


Mass: 84346.477 Da / Num. of mol.: 4 / Mutation: S99N / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2077 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaCl, 0.1 M Tris pH 7.5, 20% w/v PEG 4000, 10% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.78→80 Å / Num. obs: 282120 / % possible obs: 99.4 % / Redundancy: 4.56 % / Biso Wilson estimate: 20.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.113 / Net I/σ(I): 11.54
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 4.62 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 45601 / CC1/2: 0.828 / Rrim(I) all: 0.905 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gge

1gge


Resolution: 1.78→69.43 Å / SU ML: 0.2598 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.1948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 1410 -
Rwork0.1889 280398 -
obs0.1891 281808 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 1.78→69.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22972 0 186 2077 25235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006423855
X-RAY DIFFRACTIONf_angle_d1.091232523
X-RAY DIFFRACTIONf_chiral_restr0.05253425
X-RAY DIFFRACTIONf_plane_restr0.0064346
X-RAY DIFFRACTIONf_dihedral_angle_d21.86148903
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)
10.202413906243-0.237065615432-0.2273186696161.824835409790.8645286381850.48891183333-0.0879607269038-0.103016952032-0.1046356933920.373091735686-0.1035461304830.4474578598180.0987963045464-0.1926206468030.1630037686590.170796591903-0.02197277214310.06399478052890.2959096584-0.01679621939350.305365969378-37.0685376337-15.218680895141.7436823631
20.2606540753460.00723830490762-0.03952986425270.447036274480.2961998593410.8574278957870.00258479120588-0.04105191865430.08212167229170.00317196041892-0.02170475188470.0551285267773-0.344820622677-0.04047383500640.03010863733940.357900352402-0.03654895487980.03900613567410.142301106512-0.01138509311550.198399718798-20.25959754477.8857376497340.4994847171
30.21104584617-0.107118440839-0.2160756680670.2687014054270.2168363649110.3490406040520.0545821273770.0009822914796670.117132274559-0.05146560815950.01217951327550.0143320986127-0.4656991376950.006762772224230.003805998936620.57583768582-0.0958942398190.04119745412680.0886281399863-0.00938478369520.228285479775-13.901767431613.176973103834.8168071258
40.271394761541-0.020195396371-0.05665099366921.32739848103-0.5191579428960.231658254599-0.0201327329921-0.1936108021790.3145068558640.0724520664780.03019789625750.0681321499106-0.453255688308-0.0262861226425-0.005186803744790.773502291976-0.1095881523140.1080740238060.164263258231-0.1458172057540.29168421365-16.408574051228.447421812254.9149311272
51.97870403175-0.293643408325-0.2796484769461.653373435710.4083030813962.31392595545-0.052258346844-0.281668302978-0.1781671813780.313317796998-0.05753524168450.4178534810590.0197768055856-0.4110501670780.1700822310280.41736977452-0.01998011494680.1754801756430.313050622768-0.04814481780160.353407975286-41.4480562322-1.2086623319870.4437654283
61.6437498586-0.418389891705-0.2404944472741.369814730510.5835084177732.057022295630.0264171051429-0.372893226770.08549454372880.356626797591-0.117724711580.231348513664-0.278613472764-0.2179189849540.03893825523330.597288860391-0.03381329148610.1426770175360.323450999261-0.06884927838510.277633066885-32.730809149411.249695139374.5677809414
71.158498706120.380414549802-0.9732297843920.196185149395-0.1622564083431.6568323408-0.06410653170820.0841913744774-0.11286652473-0.04937694303720.109954342793-0.18430623480.2125389076960.7701908645150.01575513341180.1562400729440.02036439961290.003208317562840.609970074403-0.04077970765220.28385653506320.3843566848-25.385401497823.8119048988
80.232306903889-0.0310099909925-0.1496365790230.5826794229460.02950996785961.047965129260.02792751361050.0422343566550.0380178539024-0.1432437225950.0250802458812-0.112575010393-0.286662879070.3617636650470.001808716824560.346434944334-0.1413171351610.06782269355510.23331108395-0.003330496381030.2009536163276.76719075323-4.387318680969.79859933253
90.336137791057-0.106941963179-0.404712235520.4496257663760.1459590307990.3615243036830.01637520872710.05914341616960.0495692691534-0.2211896075190.0633037244314-0.0913852027556-0.4182097149040.3188326872120.06091177091910.514612309067-0.1847258080970.06733550975240.1634018827870.03614284258790.2003468960381.330601151523.9078588518710.8493844215
100.4016806445930.124950282161-0.2389099965661.75499489659-0.3551368461530.208306139388-0.04224034462150.3605805875950.171496105193-0.4557645614980.0474111632721-0.0983458417223-0.1973053238520.2253998678430.01737158218770.751946015739-0.216091056490.09687929577470.4200472835370.01657819837860.1943093701554.791524283423.28929159325-14.3492017911
112.36594998912.20527443584-1.12284532153.80377619541-2.152464399681.24648294213-0.0272659998873-0.0502332951575-0.21281636985-0.1048470067680.0539122860422-0.514983492888-0.03021030336630.677230152768-0.03222443879580.3015588435360.002848415039170.09285971095130.678287511543-0.04202233780860.28747966939225.5053273697-32.2482120117-7.34661015771
121.804841130390.251152910195-0.9931246618571.81063622651-0.800358730391.725487984580.005072998839090.139080317533-0.041500276122-0.3885921494470.00460287359429-0.168794246928-0.02421580404820.4741692284970.006331878156920.465154512224-0.0937912570640.1372970121170.469998051785-0.04000614655890.24118724082218.0858916527-24.1696681898-18.5992614113
130.173820923479-0.03524730530620.192721663821.25129495781.350616864981.88720461708-0.02749942188550.10695434834-0.00556731186476-0.450911272513-0.06841891722230.164011784873-0.37283072583-0.2134268821410.07610426438530.207534614446-0.00947018572274-0.07493983420310.259515036404-0.0115368935140.206137311681-28.058093974-9.943917432485.61107937076
140.290613735179-0.0403227803832-0.1471081266990.4600010938760.1307399495890.919385835527-0.03299525062910.0162683646303-0.0478654210189-0.0337380026969-0.003653432130830.01246011488190.0180401918990.06152248927940.03797779941230.169666215639-0.01132879340190.01520902144690.0894528467903-0.001736555647890.147782523259-10.2032981575-26.546662004515.7197425506
150.3132198873660.0328080638719-0.07983572507560.3474734309410.2345537838580.825146523351-0.06233968774230.0198248644788-0.1168104983650.00807790828824-0.01928473643740.08116413068160.218633060857-0.007855197926490.07421279019210.218260209507-0.01618875696080.03881632030430.1246800480070.001851755614870.184842749329-18.5952378793-34.100941654619.3804408029
160.1806610324650.0598036579973-0.04467380037890.4780147399360.1849874922491.03919010948-0.0562799287197-0.0140167332495-0.1202088110880.03191620257270.0383903710492-0.05449019120570.3455453921630.1969641188370.03480824189320.3624654675820.05589958398170.06297119356290.1695131073270.002088345870770.252118533841-1.07228342209-46.638621289516.6693542797
170.3396990939610.294780227920.1500805454210.88208217012-0.2789864576541.31085882058-0.1260972896920.173787336553-0.263894853438-0.03355386121450.0752267022505-0.1341129589240.3655192750650.374843337795-0.02958594075380.4866037246550.114132976150.1046831993580.245877965756-0.07181884205130.2862574314240.952076977836-52.03738653743.49062059025
181.72377508533-0.03612909448530.1103748063131.35623516430.3609438244922.48865208794-0.1386481181260.405473405372-0.0526060693435-0.4597579027680.06488799434060.03887222116610.09050111413650.04612743396610.07085363519360.472450290986-0.08534154835830.007017467001820.27898431879-0.0325415517530.182329162702-11.4873564327-31.533345255-21.2448121312
190.417424370680.0559766280009-0.5049962650010.230468879563-0.2198343992540.754009845349-0.00954672132101-0.2236866401560.09701083669790.1760325313050.136601528527-0.106574362374-0.4443445158360.627824100284-0.101461097170.387516930687-0.180432276464-0.03199867047780.484132810748-0.06857266174890.27091356835613.9500172281.6025100343349.2180153742
200.273737464255-0.0450102676628-0.08735988390620.3801234321680.2622570246051.03953257572-0.0366507968805-0.136491284696-0.03494173337130.2056557938780.0388437366196-0.01643624361190.0922786136930.2030284956410.008003189340890.314706425196-0.009434333320190.02711255324940.180238891350.02362042491270.181763074995-4.16701303398-19.182683153254.3516452691
210.189652781809-0.04380574108420.1184928716560.429852158830.1476181302490.914378516572-0.0693134707682-0.145861007504-0.08241519677330.2949562891850.02869718284180.05551914215130.2516990085070.1109018971780.03660032918620.4138641155670.01591967855290.06310261594810.1493297511710.04048195881040.208347246765-9.91381953916-27.738120682855.8588724619
221.00383766857-0.293528346061-0.3040308447160.7031186511230.1603325662621.72299532304-0.00228980320633-0.4113971050970.1911770193680.563206694149-0.00707679451984-0.10420575068-0.2138336901980.1817444085750.01280016221450.756255932418-0.0558392872973-0.02086376334540.363606616357-0.05251645789740.24722179513-4.250723741873.5698360603982.4544274225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 422 )
3X-RAY DIFFRACTION3chain 'A' and (resid 423 through 562 )
4X-RAY DIFFRACTION4chain 'A' and (resid 563 through 601 )
5X-RAY DIFFRACTION5chain 'A' and (resid 602 through 658 )
6X-RAY DIFFRACTION6chain 'A' and (resid 659 through 753 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 91 )
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 422 )
9X-RAY DIFFRACTION9chain 'B' and (resid 423 through 562 )
10X-RAY DIFFRACTION10chain 'B' and (resid 563 through 601 )
11X-RAY DIFFRACTION11chain 'B' and (resid 602 through 658 )
12X-RAY DIFFRACTION12chain 'B' and (resid 659 through 753 )
13X-RAY DIFFRACTION13chain 'C' and (resid 28 through 90 )
14X-RAY DIFFRACTION14chain 'C' and (resid 91 through 257 )
15X-RAY DIFFRACTION15chain 'C' and (resid 258 through 474 )
16X-RAY DIFFRACTION16chain 'C' and (resid 475 through 550 )
17X-RAY DIFFRACTION17chain 'C' and (resid 551 through 601 )
18X-RAY DIFFRACTION18chain 'C' and (resid 602 through 753 )
19X-RAY DIFFRACTION19chain 'D' and (resid 28 through 88 )
20X-RAY DIFFRACTION20chain 'D' and (resid 89 through 422 )
21X-RAY DIFFRACTION21chain 'D' and (resid 423 through 601 )
22X-RAY DIFFRACTION22chain 'D' and (resid 602 through 753 )

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