[English] 日本語
Yorodumi
- PDB-7ouy: Crystal structure of dimeric chlorite dismutase variant R127A (CC... -

+
Open data


ID or keywords:

Loading...

-
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


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 / Chlorite dismutase
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 7 types, 901 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene 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 / Glycerol


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


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 / Diethylene glycol


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


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


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more