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

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Basic information

Entry
Database: PDB / ID: 7ouy
TitleCrystal structure of dimeric chlorite dismutase variant R127A (CCld R127A) from Cyanothece sp. PCC7425 in complex with nitrite
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Chlorite dismutase / nitrite
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 / NITRITE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 14, 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)91,35127
Polymers86,9794
Non-polymers4,37223
Water15,817878
1
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,65113
Polymers43,4902
Non-polymers2,16211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,69914
Polymers43,4902
Non-polymers2,21012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.250, 54.960, 93.895
Angle α, β, γ (deg.)99.508, 94.805, 98.375
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,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 , 7 types, 901 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.15 M MgSO4, 23 %w/v PEG 3350, 5 %v/v Glycerol Soaking: 50mM NaNO2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.5→47.1 Å / Num. obs: 151776 / % possible obs: 90.79 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.996 / Net I/σ(I): 4.04
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 13190 / CC1/2: 0.206

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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: 1.5→30.44 Å / SU ML: 0.2634 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.3832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 1515 1.03 %
Rwork0.2491 145840 -
obs0.2493 147355 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.44 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 295 878 6969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00736260
X-RAY DIFFRACTIONf_angle_d0.74678482
X-RAY DIFFRACTIONf_chiral_restr0.0466850
X-RAY DIFFRACTIONf_plane_restr0.00841066
X-RAY DIFFRACTIONf_dihedral_angle_d12.9617862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.4296900.43529238X-RAY DIFFRACTION63.36
1.55-1.60.3931370.413612475X-RAY DIFFRACTION85.57
1.6-1.670.37931430.390613882X-RAY DIFFRACTION94.82
1.67-1.740.36381370.364114011X-RAY DIFFRACTION96.08
1.74-1.840.37361530.32114081X-RAY DIFFRACTION96.32
1.84-1.950.31931500.298414091X-RAY DIFFRACTION96.47
1.95-2.10.30211450.26913995X-RAY DIFFRACTION96.13
2.1-2.310.30451490.257313929X-RAY DIFFRACTION95.41
2.31-2.650.271400.243413746X-RAY DIFFRACTION94.07
2.65-3.330.2241400.22813583X-RAY DIFFRACTION93.08
3.33-30.440.22441310.185912809X-RAY DIFFRACTION87.72
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)
10.9842110580660.03456452328610.1838091354472.58345267155-0.9399351479811.47366159150.04520489501120.1863941773650.139848895493-0.693932986902-0.137402741465-0.401616857795-0.04858942313190.1220530667290.07236141827840.4639122396590.04350082236910.08382731905010.2322799023710.03994909459750.2025399840842.5867491141110.8152499046-11.0902449414
22.930996154070.897381721169-0.265380235713.1626857549-1.887840881842.95009540219-0.03045762862840.243715288977-0.0146333111559-0.07377540667860.4326885167670.66321929744-0.222805930961-0.0888155745748-0.07963808607590.470059991618-0.0216683804870.132822775160.3093863451120.06341341191120.4155827268434.804492394736.780118043146.8497863734
30.2817751715660.454800785831-0.4149548698231.24195922483-0.8114295973691.53955026593-0.0163710986904-0.28762456407-0.1065412098141.029993422130.1181114726920.4079612526040.180979855328-0.167764584460.08196644473280.6677651630680.01358735473010.2355283759010.3058206422960.09124177463990.2922786670897.075313231165.1556514572655.8697094282
41.598928416280.719946142405-0.595784376614.14523692067-1.175883842221.55903194938-0.047564687487-0.0935806920158-0.1434861320580.347513278678-0.13573525335-0.4342978823670.06172987486560.1276372871260.1560900152590.3504708743460.0301813614667-0.06133278980270.2203213222370.03584577803790.19375047708322.42738173187.717154706950.2267596387
53.29840924697-1.379079429911.158207993350.614716591531-0.8276062441353.25969840843-0.1312798030890.07746422030090.1740059718440.480547369782-0.168489727651-0.947985121621-0.06904131929780.3842772048940.05300045612710.4022651990460.0301511682619-0.1886237498380.380575239010.2099286739380.5340720526431.22889221745.501502051253.7210427617
61.139934109370.0919204909984-0.1977523191321.93694025023-0.5737437642862.097848305180.0479023343252-0.212500890765-0.1428912600981.12565636753-0.13366640167-0.1596831331930.1145300761530.049359526508-0.02168071524060.5652149850950.0266591490879-0.02778875891350.2671624146980.0632792176880.20235087313717.53983096964.3424609809857.0383715206
75.67323759995-1.19684097724-0.166665171047.19643576681-1.829365651995.20839686480.171773369348-0.6957269959250.1519254895580.5309213291850.2074793653470.6048735966210.317586846609-0.0382132139784-0.328327673530.3258855742940.07092994083030.08105436344430.3391683436610.06406809970030.405614802844.6120653218428.418843835942.0542551898
81.984382010440.733737591871-1.044146839931.594097993050.9838885954542.000203827940.2119369348190.3340587764270.296213967559-0.6083436045820.09922339183080.680790210110.0737463360086-0.3128441090230.2264867961750.4670688737680.0987069776828-0.1668072909180.2660392736930.1046964415110.3122458688424.2635309346733.499130914226.179039204
93.84459245874-3.759282246271.479898045713.83588970673-1.105811443171.357372560310.153202943274-0.411790354744-0.2457586827770.1457862031610.4666003499940.9776154257140.0256784819046-0.786434701146-0.4269895187230.2752545378920.0461411728945-0.03429495912140.2914770737080.1172031688280.4666095397331.2664061420729.064300021336.5610557459
100.961702784853-0.114512744648-0.0755775771974.16157678422-1.282930219781.188547463130.0846001732393-0.07515622023660.2025543906690.375382705899-0.171336109446-0.337206103186-0.341531466182-0.0149012459490.1581450308770.354119607135-0.0162415943065-0.03007935526520.1644820132390.01147427864390.18430739018722.38964775234.092164612843.7434246596
110.6727036286750.000616845325769-0.03963310523512.78734108317-0.6940350113031.083587046460.08903077862140.1987809066110.0574311357122-0.737992780065-0.265562997306-0.6228794902420.1951535545060.1979799590170.1296972821080.332525468280.08086961661660.1198516432970.2221509038280.07177848526210.26382516010524.840348687223.124086605633.5119368505
121.19081954850.34497798616-0.1298969925193.42514963017-0.8858245767441.957375895880.1050523417680.1136456645250.114054219583-0.656277597084-0.136501570457-0.141410378232-0.09463895358520.08029149733260.01172695903760.2891151517450.04857493057070.006021163229460.1958292742430.03517674053080.13955803028516.432830144331.343110308731.3599841672
134.871699475860.925891004764-0.1384617121826.095619167580.1799430634184.17948313639-0.168648855687-0.0371556722196-0.161878608770.2056626548450.1493418053320.3500647071970.09919971808-0.4135311451380.009890265276040.2240278388680.02462850046210.04581004023640.1794520170330.02333848760640.222769422101-14.0474662634-16.83778039577.62713637577
143.480815730531.69128270411-1.490193253584.481370649180.2618912363552.42569810925-0.0400555694972-0.000976398990003-0.02028295915590.3123588796750.09162201860070.8922747771580.153834802166-0.439649902772-0.004378848779780.3004950595750.0630867328670.1246352134790.1937015751170.03375406700630.321726951444-15.3847367788-12.28285099710.7738997412
151.773372951891.01443546272-0.6165503062313.90758830893-1.718054655031.28766891151-0.0560002906808-0.0162798376346-0.1679777018370.0799463036076-0.152655086619-0.6391511434160.01888426752120.0812737121840.1928349937110.2292330921470.0418542450354-0.035320547050.1799695131160.02526798003030.2038018787463.96093931505-10.30858074413.63137234615
161.39486738120.6216359995640.1689271465332.91458591012-0.4638358949132.076615549390.002588092649210.0305273867248-0.05499209467950.232402936642-0.141647329059-0.6419401026390.04029461295780.2205195958990.1173553965070.1956141640070.0130289033615-0.02730752656260.1703193543390.02693357415840.1911520414711.3064080367-12.48875500926.75270048749
171.959879674470.07531092155690.1116893515051.64169603205-0.02893498246831.98148555103-0.0239679691201-0.343333269242-0.3085670029380.608186759244-0.0688439071487-0.4293678285690.07586894325440.1937112088080.08606455531640.4097621007790.0155782500247-0.09783731439720.2879021386230.08009721978750.2622673602140.379592589484-16.046215739914.9573127177
188.94012645724-2.878375479252.9331226564.34538361409-6.050295228178.59964746591-0.188823383138-0.520867850810.190683486979-0.0440320029980.07801477105010.823083588863-0.20505310608-0.3273319475790.05025983215320.4518686990.0599246301454-0.04472623346110.225004081280.008285365631560.40893756253-13.47989460729.74050499608-4.51328540406
191.004414557280.770928831165-0.8945468297250.946961272894-0.3644087265261.139712603420.003756980095570.4333303207340.468818005583-0.6274231233890.1858800157950.431912197785-0.0211527937244-0.3413209478910.3135818920790.7893060211010.118651093125-0.198181577330.3948795678130.1213969626120.30786409748-13.547347137515.0635087845-17.9222998949
201.08201869677-0.04267240546050.9434027817791.91136035999-0.6619297061261.60010804269-0.0575011597344-0.07996388944130.180338334395-0.354369656430.1808784903771.26079205056-0.19852360064-0.780494936806-0.3898977965870.5766688484080.0727992582011-0.2289761513280.3929858911880.06415867785540.530786359927-16.29829913487.43377494305-11.1168693542
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 56 through 182 )DU56 - 18250 - 176
22chain 'A' and (resid 1 through 10 )AA1 - 101 - 10
33chain 'A' and (resid 11 through 63 )AA11 - 6311 - 57
44chain 'A' and (resid 64 through 108 )AA64 - 10858 - 102
55chain 'A' and (resid 109 through 121 )AA109 - 121103 - 115
66chain 'A' and (resid 122 through 182 )AA122 - 182116 - 176
77chain 'B' and (resid 1 through 10 )BH1 - 101 - 10
88chain 'B' and (resid 11 through 32 )BH11 - 3211 - 32
99chain 'B' and (resid 33 through 55 )BH33 - 5533 - 49
1010chain 'B' and (resid 56 through 83 )BH56 - 8350 - 77
1111chain 'B' and (resid 84 through 121 )BH84 - 12178 - 115
1212chain 'B' and (resid 122 through 182 )BH122 - 182116 - 176
1313chain 'C' and (resid 1 through 21 )CM1 - 211 - 21
1414chain 'C' and (resid 22 through 55 )CM22 - 5522 - 49
1515chain 'C' and (resid 56 through 108 )CM56 - 10850 - 102
1616chain 'C' and (resid 109 through 148 )CM109 - 148103 - 142
1717chain 'C' and (resid 149 through 182 )CM149 - 182143 - 176
1818chain 'D' and (resid 1 through 10 )DU1 - 101 - 10
1919chain 'D' and (resid 11 through 38 )DU11 - 3811 - 38
2020chain 'D' and (resid 39 through 55 )DU39 - 5539 - 49

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