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- PDB-7ati: Crystal structure of dimeric chlorite dismutase variant Q74V (CCl... -

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Basic information

Entry
Database: PDB / ID: 7ati
TitleCrystal structure of dimeric chlorite dismutase variant Q74V (CCld Q74V) from Cyanothece sp. PCC7425
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / chlorite dismutase / heme enzyme
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSchmidt, D. / Mlynek, G. / Djinovic-Carugo, K. / Obinger, C.
CitationJournal: Biochemistry / Year: 2021
Title: Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis.
Authors: Schmidt, D. / Serra, I. / Mlynek, G. / Pfanzagl, V. / Hofbauer, S. / Furtmuller, P.G. / Djinovic-Carugo, K. / Van Doorslaer, S. / Obinger, C.
History
DepositionOct 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,60212
Polymers43,6042
Non-polymers1,99810
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, HPLC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-41 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.014, 72.676, 60.169
Angle α, β, γ (deg.)90.000, 112.733, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Chlorite dismutase


Mass: 21801.883 Da / Num. of mol.: 2 / Mutation: Q74V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 7425 / ATCC 29141) (bacteria)
Gene: Cyan7425_1434 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8HNS6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, pH 8.5, 0.2 M MgCl2, 20 w/v % PEG 8000

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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: 0.976252 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 1.51→36.34 Å / Num. obs: 68450 / % possible obs: 98.28 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09327 / Rrim(I) all: 0.1012 / Net I/σ(I): 11.45
Reflection shellResolution: 1.51→1.564 Å / Num. unique obs: 6796 / CC1/2: 0.169

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Processing

Software
NameVersionClassification
PHENIXdev_3885refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MAU

5mau


Resolution: 1.51→36.34 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 1575 2.34 %
Rwork0.1749 65798 -
obs0.1754 67373 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.82 Å2
Refinement stepCycle: LAST / Resolution: 1.51→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 136 406 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01823288
X-RAY DIFFRACTIONf_angle_d1.72644480
X-RAY DIFFRACTIONf_chiral_restr0.1022453
X-RAY DIFFRACTIONf_plane_restr0.0166572
X-RAY DIFFRACTIONf_dihedral_angle_d22.2567458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.560.3721180.39115034X-RAY DIFFRACTION83.2
1.56-1.610.33521500.34556029X-RAY DIFFRACTION99.29
1.61-1.680.35711380.3146045X-RAY DIFFRACTION99.84
1.68-1.760.31311500.2936046X-RAY DIFFRACTION99.9
1.76-1.850.29631510.25046039X-RAY DIFFRACTION99.66
1.85-1.960.25571380.2076087X-RAY DIFFRACTION99.94
1.96-2.120.21011490.17356069X-RAY DIFFRACTION99.94
2.12-2.330.1971420.16536053X-RAY DIFFRACTION99.84
2.33-2.670.19721440.16566102X-RAY DIFFRACTION99.89
2.67-3.360.1711510.16266118X-RAY DIFFRACTION99.94
3.36-36.340.14791440.13866176X-RAY DIFFRACTION99.76
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)
10.532180143175-0.218273743969-0.3692344963160.1788883323520.2512916438170.3682171228260.0264124583873-0.318055923967-0.177638501780.136688006484-0.171826401302-0.1759425344950.747659067577-0.0813581293997-0.003060949302210.386372117384-0.0778594820296-0.005438822233340.1647824316130.03590965300130.2557759425245.33863806654-9.275391496622.84156374277
20.4450415912230.0542472015197-0.04649044669530.142017215675-0.0372247970230.394634325898-0.2859522814180.2711822910520.127490704182-0.4869511120980.2887932166630.2090846036980.0563899730597-0.4442472605620.00232323836030.36446482426-0.105010536941-0.02454428022470.2695738055590.04477326010130.251300199457-3.50432539804-2.72074227802-9.4934889388
30.489128724784-0.2344382567460.0230993153140.128728299788-0.04339422820640.1683087378130.08760596059360.385118821358-0.052552877549-0.02040118398470.01614470323580.02150370587170.186839701245-0.1109610251590.0131806878280.34007577177-0.071158094499-0.006337667594140.1701534792130.02180394665870.2228481031063.30514172576-1.19260914609-9.42301049676
40.309245188361-0.1766845498820.353703675360.209165502792-0.3814999403980.701062562209-0.1315427532460.574158890322-0.734701834349-0.421090075132-0.476140106854-0.6005375761670.6852030970610.2701288480080.03585993481450.4530411081420.01212249612270.1155810289290.412432073181-0.01570357780840.485695570058.36706499558-12.9461047243-6.72423405667
50.6618768780190.2707236519230.123327027320.423314498025-0.2736987357790.3659615110460.0198200154524-0.265037829788-0.127859172536-0.265730859835-0.02760290043280.0267454249406-0.116681322398-0.1415655961112.33160927807E-50.2518593335750.01200811312210.004087786986860.2632511894470.01047271849980.1980713185098.74657493615-0.4205969708387.61126068114
60.126239706834-0.0391886685637-0.1498505874690.3332047694420.1603179197840.1911941891870.0889238263389-0.380916137916-0.118570055980.1225535510210.0899654633888-0.05727408339350.065565959733-0.1120668714995.14407899783E-50.261931829394-0.03944264210790.01829290567950.5157923073960.05890750838770.279158298728-6.871244942362.2761111005913.6338032051
71.123280297840.2700301269880.4751634664571.445811523540.1282378570031.7838681014-0.065459742675-0.1702954493560.1380474638720.007228374489210.02853733606780.0384638432707-0.0895375283715-0.1415725616974.63930477716E-50.1912884037450.01883217299640.01027350763950.16065355962-0.009244551641240.1975847157486.262574726618.052388003446.6916249458
80.122219093125-0.175428947620.03244559412620.377685563042-0.05284281306950.23460223153-0.111844239253-0.230486009838-0.01245048729090.0005985190204940.08231141908120.289363802519-0.144569906848-0.3529326343688.30650022848E-50.2531942386640.038015561239-0.0356731017940.2275665214630.01294359729950.355053222674-6.0238908280513.38270794790.872656687963
90.317997342526-0.262697395857-0.2235112031010.528532121468-0.08422701314341.30690907456-0.0100431786227-0.1315786638840.121061647325-0.0350278577456-0.002684396065450.0715034081779-0.0261272264467-0.1983663910061.72638456387E-50.228844253436-0.01859852794469.62194790014E-50.1776359368370.02523294368760.2383479462713.393338738617.82194091525-2.31153674327
100.21499310340.1224360149750.05067933429310.1970009618090.2060904479960.2431527399770.2373599740480.375986685951-0.244052430856-0.3025619388370.0430075361981-0.1448890550910.1830938686820.134075790604-0.0002217144021390.3473564033890.04674413664770.01756616967410.3281163042780.03400796037790.29701598816327.3222631147-9.541298904678.59405291361
110.6062692611690.7657437551290.5795223385121.104576144060.4599099734521.279020893260.460792975434-0.188179345786-0.8993735991880.03891859775060.244255491417-0.4979805574260.7154596377720.2440688066280.411469782820.488283977490.0772503930469-0.08786549667210.2965750092470.2576392673490.46904099342132.5388933557-17.37935216120.2624288708
120.009632549742210.025095319648-0.01715927260810.0475912069657-0.0382683220840.0268891812460.4388203143290.416266707253-0.563585471124-0.3808288977530.3407202588010.2798670811790.806295581047-0.246256780764-5.84657747013E-50.8882518629580.0247352208769-0.1647120841130.42065746892-0.02914559243610.89694893320427.3082217467-20.32334350817.48377382861
130.7790772343690.1399533628850.1231198465210.175924865814-0.2625124453220.542373180748-0.00708217493974-0.301288796755-0.2080012665030.0709628791044-0.0229334261994-0.1709046196660.352198978122-0.108364764897-0.0001224655745080.2820699096380.00190311364910.008269676911580.1976263413520.04341983783570.24777972391421.276957225-3.1434003151714.5593255261
140.576235678247-0.3159901623020.3633430511630.4095345500460.2936733119261.025409751230.0180627134466-0.2773931132090.20062881213-0.122581002926-0.111788475649-0.148795880741-0.07077379556310.12865113565-2.38765834527E-50.234156428068-0.0184691127675-0.01900010094810.3028631691220.0477967193110.30001825906332.09009281452.5251336204419.3065115496
150.236934825343-0.199663112740.07116086016280.2276290531690.03433371417610.132973288123-0.0806200935163-0.78285703928-0.01226350994330.1909664408940.06725251166840.2808768357470.122247502308-0.659667953745-0.001542450461170.2510802224920.00439783360610.03202011668740.5192384162430.01281297910490.23273047356210.8404749212.4415612602925.6520077246
160.1274233731920.08916216596180.007601000820590.16745168995-0.1213138961040.1432347219880.108364277407-0.5469720775610.4112032289340.122788507107-0.268045873256-5.28812475113E-5-0.564209815947-0.352783130254-0.0004096378513420.330221816950.0463755233381-0.01514532683430.434132304783-0.07496206341840.27755895508124.29870518967.7788176854729.9422475237
170.821981946794-0.581312387670.4027236212550.83085590666-0.346543230831.232864174520.0129667579938-0.473794836792-0.05661644697030.0733686978525-0.0594540226259-0.101676056660.104383084064-0.0288144878542-1.41117525638E-50.235932318623-0.0326302882139-0.004648353952410.3074747964620.06661762573020.21874530354228.3992199203-3.3091904262923.7524993052
180.3293139585370.1305289235960.4786905886710.8817814588520.23232131490.6530978927320.140762734375-0.468205702584-0.1478218723420.146821790677-0.0768675763461-0.1454714942290.3384855153520.0411366282815-3.1473173232E-50.295455788672-0.0253242862335-0.006089512164370.4148433744770.1274172286490.28792892715426.8230649201-9.0488820300825.8213894282
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 10 )AA1 - 101 - 10
22chain 'A' and (resid 11 through 21 )AA11 - 2111 - 21
33chain 'A' and (resid 22 through 37 )AA22 - 3722 - 37
44chain 'A' and (resid 38 through 49 )AA38 - 4938 - 49
55chain 'A' and (resid 50 through 63 )AA50 - 6350 - 63
66chain 'A' and (resid 64 through 83 )AA64 - 8364 - 89
77chain 'A' and (resid 84 through 148 )AA84 - 14890 - 160
88chain 'A' and (resid 149 through 165 )AA149 - 165161 - 180
99chain 'A' and (resid 166 through 182 )AA166 - 182181 - 197
1010chain 'B' and (resid 1 through 10 )BH1 - 101 - 10
1111chain 'B' and (resid 11 through 37 )BH11 - 3711 - 37
1212chain 'B' and (resid 38 through 49 )BH38 - 4938 - 49
1313chain 'B' and (resid 50 through 63 )BH50 - 6350 - 63
1414chain 'B' and (resid 64 through 92 )BH64 - 9264 - 92
1515chain 'B' and (resid 93 through 108 )BH93 - 10893 - 114
1616chain 'B' and (resid 109 through 121 )BH109 - 121115 - 130
1717chain 'B' and (resid 122 through 166 )BH122 - 166131 - 178
1818chain 'B' and (resid 167 through 182 )BH167 - 182179 - 194

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