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- PDB-7owi: Crystal structure of dimeric chlorite dismutase variant R127A (CC... -

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Basic information

Entry
Database: PDB / ID: 7owi
TitleCrystal structure of dimeric chlorite dismutase variant R127A (CCld R127A) from Cyanothece sp. PCC7425
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Chlorite dismutase
Function / homologyHeme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Chlorite dismutase
Function and homology information
Biological speciesCyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchmidt, D. / Mlynek, G. / Djinovic-Carugo, K. / Obinger, C.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP30979 Austria
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase.
Authors: Serra, I. / Schmidt, D. / Pfanzagl, V. / Mlynek, G. / Hofbauer, S. / Djinovic-Carugo, K. / Furtmuller, P.G. / Garcia-Rubio, I. / Van Doorslaer, S. / Obinger, C.
History
DepositionJun 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,80321
Polymers86,9794
Non-polymers3,82417
Water13,763764
1
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2499
Polymers43,4902
Non-polymers1,7607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,55312
Polymers43,4902
Non-polymers2,06410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.447, 72.675, 112.120
Angle α, β, γ (deg.)90.000, 94.835, 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Chlorite dismutase /


Mass: 21744.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. PCC 7425 (bacteria) / Gene: Cyan7425_1434 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8HNS6

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Non-polymers , 5 types, 781 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 51.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M TRIS pH 8, 20 %w/v PEG 6K, 0.2 M MgCl2, MPD (Cryoprotectant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→44.29 Å / Num. obs: 95807 / % possible obs: 99.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.05 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.74
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 9516 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MAU

5mau


Resolution: 1.7→44.29 Å / SU ML: 0.2201 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196 1177 1.23 %
Rwork0.1733 94537 -
obs0.1736 95714 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5927 0 262 764 6953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826400
X-RAY DIFFRACTIONf_angle_d0.84188715
X-RAY DIFFRACTIONf_chiral_restr0.0528887
X-RAY DIFFRACTIONf_plane_restr0.00791103
X-RAY DIFFRACTIONf_dihedral_angle_d13.2364876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.780.33711510.305211729X-RAY DIFFRACTION99.92
1.78-1.870.24681410.244311815X-RAY DIFFRACTION99.99
1.87-1.990.27031480.222811701X-RAY DIFFRACTION99.8
1.99-2.140.21581490.190711817X-RAY DIFFRACTION99.89
2.14-2.360.1951400.167511794X-RAY DIFFRACTION99.83
2.36-2.70.19581460.174111832X-RAY DIFFRACTION99.94
2.7-3.40.21181490.164911877X-RAY DIFFRACTION99.98
3.4-44.290.15761530.147611972X-RAY DIFFRACTION99.53
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)
12.853996860510.493471347992-1.589568156521.02651258688-0.7788843942935.435010521380.17889251194-0.1093220271210.0516000855733-0.0368905613885-0.0434798444415-0.097058213034-0.4230353847110.1714562631590.002750171232860.3516547968820.008313361575060.01112837421680.1459246686530.01321064633330.280866168377-21.923953910122.8812255077-1.5424320033
25.75879098606-1.329064323130.4817510123162.28454927526-0.4790056111754.75124062115-0.130142131982-0.4139013814920.07445152911240.5098535564240.03029292211280.107466809777-0.197334889268-0.4178624927740.007652602853350.3059662293730.01800646686380.0436408209640.283430960399-0.003338578710970.194309003972-30.280150057515.9532511899.78293788332
33.39862170878-1.054637264520.2867025807043.6040178489-0.8373318885963.102136892890.00234189416549-0.315638616533-0.005878523591790.2472861431670.1417496239290.273320632586-0.215506045399-0.0633196925246-0.07805784528990.271127746483-0.00857560768564-0.0007148558838680.207248457872-0.002125848206580.185958808247-24.223532280515.69191449839.38326696008
42.35674523010.0510530121049-0.9123388008991.9330421826-0.03122035442433.54854584997-0.00493798907327-0.2209038770160.2865700723630.184775914510.0672854957788-0.144836825616-0.348057065580.193156253936-0.07201102152170.2594343137810.00753498027343-0.02508451406110.201271979664-0.005459943482490.245336415331-18.841967168319.55212481-1.61403504679
51.233632271050.177947549789-0.6863196976930.3387509747380.3540376561541.257730345410.004252522036450.2274939832810.126041058338-0.09435530619570.0440023240840.0470571230119-0.0921444485492-0.35523342297-0.05359960742270.2424521820220.0103254381587-0.0168889305820.2922802154150.04686545157690.248598390205-31.1726926310.9987804651-8.96671665851
61.689581917711.10250454788-1.164505054343.342775171192.177122080424.63655290289-0.1912140378380.0714466513358-0.16397546723-0.1673094462090.0921314183929-0.1887160069910.405835337580.3632794737960.0879010448680.2861292313110.01383719873770.04064462938140.2225987056950.02224949258270.263393943053-11.92824270540.457804753804-11.1548210374
74.50186640101-5.79846727264-1.494273093128.205627823231.32492171013.656005961130.2058898361970.590047524931-1.00196423516-0.273287009287-0.3620130883340.2842722770620.116698651614-0.00509983852930.1566628418390.40462664844-0.06264363630010.01590306694250.270366359253-0.00817455791590.32049960231-26.0586225134-2.2301039955-12.601479341
83.00939393534-0.0676130024756-1.606990161661.92212857607-0.3496951034441.712644139920.01250259626670.1145268327480.01475103412260.0664139332717-0.012445752067-0.0123751893689-0.0801075656926-0.1125711723160.02406239903980.1882039032390.0108329754972-0.005640345915680.192229245550.01154459283680.146902380407-24.16881486711.8248520374-3.98956608078
94.89825490271-2.47432305948-1.563812996264.460674110470.7426031876052.2582183990.03398412955780.140076021065-0.0461402737728-0.00874099117929-0.006709836518270.1350250632270.226794872026-0.199786816830.04955346232750.229151268885-0.04504789808310.01929614736150.2153160136770.01207462230830.254612947789-34.00486286440.62373918425-0.735710283603
101.6223143562-0.5825256364860.2020890885441.77162975192-0.3482776723192.46894249789-0.0827184057151-0.0270382448171-0.01636155035490.09438342977470.0519158190814-0.06676145652230.107062944386-0.1284825814810.03559258304620.192300496821-0.01750929760660.01367983087260.1738011212780.03244605999330.194302264104-24.77879554046.525693604261.97750696906
113.396095148270.35903355592-1.300267766652.90669018684-1.68462848592.561648749610.123633170351-0.1544106024360.423581026190.300698701947-0.316844351572-0.365188738428-0.2810752834990.3708460066280.1490643956350.318764027877-0.0950389152537-0.1114723036830.2865973053170.08332724739640.3623222638094.5648591950228.5521586255-14.6443215701
122.322048959631.22150043464-0.8718710748333.13006915357-1.563170295621.652361037440.197181411485-0.1054100776880.463186104730.515499559124-0.206828513091-0.0482984829721-0.4185888771930.1679646702270.1009447480630.285773348946-0.0304691079038-0.0333733497820.217433170140.03947182354420.30343858737-2.0156130223327.5910025577-14.7429448023
132.757839443442.1259193878-1.240164349992.865307332690.1312354039051.52795182070.168505350850.213313397607-0.4200402829560.055845926124-0.273720582908-0.4031682397490.2897818969440.1836125667720.1222744026470.3287688140240.03062646629180.04357731212820.2800186501890.03451294335630.3490592523980.8336899955020.492331821569-19.1863307384
143.70888707631-0.6934294952281.458373268420.907570290661-0.4692654289551.38074202272-0.2240544525470.1977211090010.04649754356260.08642009578410.0411505316531-0.21821231844-0.0170177304490.1730951778150.1492650094910.231514961869-0.01307901391420.002724142059970.2877544195970.06894492046810.3171514678116.3476295049318.0609708742-19.2952537594
153.979274460231.24286725626-1.279615575374.45299374670.2688115146493.03180186312-0.2511471681240.46940705335-0.0768183955989-0.1170071395820.1437114067160.2536666682860.195962070224-0.26781511580.09548770384850.245858110624-0.0391547692072-0.02207155297490.3319179643470.02805895728670.215357415615-16.506496737112.1116001518-25.3218350454
162.76898295991-0.141094492785-0.8553117441351.4709696269-0.1440979050351.97154602751-0.1375328145680.1737136602380.00899133641094-0.0786124048563-0.0535058164211-0.1033028297350.09351086518440.1228885625440.1574863413640.231992719716-0.0189137638430.007275014356470.2474678265190.05794027607370.233829673609-1.9643449778815.3652329794-22.0058261939
175.856275458652.025846441842.299767548761.999500692630.6650366397643.60099863474-0.2592877131380.688529384393-0.0200038400881-0.3214109864580.122479269141-0.136330829697-0.1218825765890.6465594558110.1548649659650.34555013674-0.02974936538340.05919351486610.4257966325520.0627037712260.2472846522955.7828363357216.6508830873-31.2823954269
182.281803555410.4722069147960.5580960035062.074381379250.1789881989161.77240861421-0.03499423893360.2064310785430.160952711284-0.0330796309081-0.0718686508464-0.07996390677510.1047124287230.01800799449820.114073132490.249426882593-0.0195754648512-0.008357389763960.2938669044510.1146923253510.244733512872-1.5542989752422.6824800597-26.1900490825
191.263908965740.353813634324-0.7848857975361.27578380347-0.6928381502643.053237580260.03968726539930.1504614261610.123983634185-0.1171033771370.036196692743-0.0333633560478-0.351501682654-0.00202604605134-0.04411532503740.244683440403-0.0224380253182-0.00683113858660.1972669823620.003414335365670.200451911450.28889723836153.7766999645-58.7823365005
201.693126629411.80529738699-2.588543277622.61869363087-3.654068727045.073870260250.0496669398426-0.3226800992210.1286203649180.059031703868-0.04562444003270.124185736823-0.1227631384790.44220656889-0.03579927637870.231923051251-0.0517396488687-0.02154684995310.3168859653110.01353370229330.25487595991511.546655448246.6692643285-42.1827839476
211.266685655660.199031298173-0.600080048951.01797980875-0.3495624572641.53084258222-0.057835611544-0.0125125402617-0.0759768782122-0.01296915411460.00160858260245-0.01423678139310.03083717512410.04577080750460.05939648959920.1937124354150.00131033733097-0.007852271321170.171142211394-0.006512573584950.175053897058-1.6745877095241.1362706417-48.806446286
222.047898476831.04764495223-0.3583323712062.36681312093-0.5316040627271.73392135718-0.06012166335150.0150536709063-0.0821890058375-0.1294707803540.00945573824502-0.1892294549160.1162399197990.1902447786880.05199392545690.2285669183440.01505133333340.009989529521010.207646676571-0.01413386287760.2061586326145.4284792905738.7936458108-56.4503137826
233.65205605425-0.268610258498-0.9882283922813.023471949130.9421518800012.056476909380.1584560590620.224720045970.447905379158-0.146337762539-0.1110735175380.349820319178-0.4255513513-0.3242663605010.02318348136940.324130570710.0840662337257-0.02941252864190.2764205559690.01096006525510.350048004749-27.498036901563.2853022963-40.5499676526
242.5022200878-1.3947943113-0.7960251731113.374507468810.6858575721122.050350225870.1224855714240.08221267775020.448760550824-0.23906283888-0.06454354086060.0576159151272-0.409003902721-0.181803663995-0.09586943090480.2388206278020.016203396101-0.02142902965410.197474499719-0.009487170167630.297645877261-20.99258282661.8731862808-40.0185136926
253.47027595851-3.142746337371.008619157752.89352761562-0.9716359459560.3440782612570.06922891400730.2697425489070.0637595430422-0.0662900078744-0.1549369739380.008958367483420.0899166785681-0.06980187299080.100513281560.224205749753-0.02681318305350.02854007807440.26381108714-0.0147823099870.289750927464-29.201054055541.5357049541-37.7487451719
262.47675934873-0.247136238245-0.7215594508161.338226540270.1459342821451.17163623535-0.0476552736824-0.1984623015410.1074315075250.0860408472294-0.001059529499190.0104345192644-0.03158931974870.03599577313160.0415454578160.196271821396-0.00782762609627-0.009488573966970.192967565566-0.02893971553370.160073798701-16.987337645550.1596383105-32.4513298037
271.46555966351-0.180231235477-0.4761396523712.27719610905-0.07017977818632.56519881368-0.137959111348-0.3043907962260.1943328883670.2746608053480.06168841902630.098075623306-0.160354074738-0.09181032703890.0532789201670.2557980914680.004098127815970.01678711022420.265775858138-0.05341654860240.212056142151-24.674476842354.7105046411-26.8358546297
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 10 )AA2 - 101 - 9
22chain 'A' and (resid 11 through 22 )AA11 - 2210 - 21
33chain 'A' and (resid 23 through 37 )AA23 - 3722 - 36
44chain 'A' and (resid 38 through 63 )AA38 - 6337 - 62
55chain 'A' and (resid 64 through 92 )AA64 - 9263 - 91
66chain 'A' and (resid 93 through 108 )AA93 - 10892 - 107
77chain 'A' and (resid 109 through 120 )AA109 - 120108 - 119
88chain 'A' and (resid 121 through 148 )AA121 - 148120 - 147
99chain 'A' and (resid 149 through 164 )AA149 - 164148 - 163
1010chain 'A' and (resid 165 through 182 )AA165 - 182164 - 181
1111chain 'B' and (resid 2 through 21 )BE2 - 211 - 20
1212chain 'B' and (resid 22 through 63 )BE22 - 6321 - 62
1313chain 'B' and (resid 64 through 73 )BE64 - 7363 - 72
1414chain 'B' and (resid 74 through 92 )BE74 - 9273 - 91
1515chain 'B' and (resid 93 through 108 )BE93 - 10892 - 107
1616chain 'B' and (resid 109 through 148 )BE109 - 148108 - 147
1717chain 'B' and (resid 149 through 164 )BE149 - 164148 - 163
1818chain 'B' and (resid 165 through 182 )BE165 - 182164 - 181
1919chain 'C' and (resid 2 through 63 )CK2 - 631 - 62
2020chain 'C' and (resid 64 through 83 )CK64 - 8363 - 82
2121chain 'C' and (resid 84 through 148 )CK84 - 14883 - 147
2222chain 'C' and (resid 149 through 182 )CK149 - 182148 - 181
2323chain 'D' and (resid 2 through 21 )DQ2 - 211 - 20
2424chain 'D' and (resid 22 through 63 )DQ22 - 6321 - 60
2525chain 'D' and (resid 64 through 83 )DQ64 - 8361 - 80
2626chain 'D' and (resid 84 through 148 )DQ84 - 14881 - 145
2727chain 'D' and (resid 149 through 182 )DQ149 - 182146 - 179

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