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- PDB-6xuc: Structure of coproheme decarboxylase from Corynebacterium diphter... -

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Basic information

Entry
Database: PDB / ID: 6xuc
TitleStructure of coproheme decarboxylase from Corynebacterium diphteriae in complex with coproheme
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE
Function / homologyHeme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / Chem-FEC / Uncharacterized protein / Chlorite dismutase
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8702 Å
AuthorsMichlits, H. / Lier, B. / Pfanzagl, V. / Djinovic-Carugo, K. / Furtmueller, P.G. / Oostenbrink, C. / Obinger, C. / Hofbauer, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29099 Austria
CitationJournal: Acs Catalysis / Year: 2020
Title: Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation.
Authors: Michlits, H. / Lier, B. / Pfanzagl, V. / Djinovic-Carugo, K. / Furtmuller, P.G. / Oostenbrink, C. / Obinger, C. / Hofbauer, S.
History
DepositionJan 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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
C: Chlorite dismutase
D: Chlorite dismutase
E: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,98710
Polymers136,4455
Non-polymers3,5435
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21250 Å2
ΔGint-150 kcal/mol
Surface area41160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.021, 123.157, 77.893
Angle α, β, γ (deg.)90.000, 98.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chlorite dismutase


Mass: 27288.961 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: B11Q_01470, BT093_04375 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: A0A2T1BSE4, UniProt: Q6NGV6*PLUS
#2: Chemical
ChemComp-FEC / 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX / FE-COPROPORPHYRIN III


Mass: 708.538 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C36H36FeN4O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 170 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, MgCl2 / Temp details: cryo stream

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Data collection

DiffractionMean temperature: 170 K / Ambient temp details: cryo stream / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.603→48.1297 Å / Num. obs: 139066 / % possible obs: 93.6 % / Observed criterion σ(F): 1.33 / Redundancy: 3.19 % / CC1/2: 0.996 / Net I/σ(I): 6.21
Reflection shellResolution: 1.603→1.661 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 8944 / CC1/2: 0.134
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
EDNAdata reduction
EDNAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTZ
Resolution: 1.8702→48.117 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.67
RfactorNum. reflection% reflection
Rfree0.223 4520 4.9 %
Rwork0.1647 --
obs0.1676 92273 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 205.95 Å2 / Biso mean: 43.6686 Å2 / Biso min: 19.61 Å2
Refinement stepCycle: final / Resolution: 1.8702→48.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 405 568 10325
Biso mean--45.94 37.07 -
Num. residues----1147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8702-1.89140.33311200.3273205970
1.8914-1.91370.34041690.29592934100
1.9137-1.9370.32991620.28542921100
1.937-1.96160.30141560.26522944100
1.9616-1.98740.33121530.2608294599
1.9874-2.01460.32791380.2469294099
2.0146-2.04340.26851550.2386298199
2.0434-2.07390.31111190.2291294399
2.0739-2.10630.2741660.22352951100
2.1063-2.14080.2621430.22332966100
2.1408-2.17770.27771590.19632949100
2.1777-2.21730.27711410.19132927100
2.2173-2.260.22921430.18212996100
2.26-2.30610.24181640.16772922100
2.3061-2.35630.23171680.16622981100
2.3563-2.41110.22321520.17142932100
2.4111-2.47140.2551600.17092950100
2.4714-2.53820.24481500.17492962100
2.5382-2.61290.23991380.17722969100
2.6129-2.69720.22821520.1645296799
2.6972-2.79360.25431410.16632984100
2.7936-2.90540.22791580.16812935100
2.9054-3.03760.21151490.1677294599
3.0376-3.19770.20561320.1659297499
3.1977-3.3980.24931490.15622976100
3.398-3.66030.22121450.14294899
3.6603-4.02850.17761650.1278293799
4.0285-4.6110.17641730.1159290398
4.611-5.80780.16851440.12772987100
5.8078-48.1170.19481560.1609302599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6195-0.0212-0.43130.56130.01390.3123-0.09280.03340.12080.11620.0230.1009-0.1148-0.0206-0.00020.3273-0.01410.01040.35760.00750.314432.189979.442481.7253
20.35750.19080.18890.5530.42680.3329-0.0418-0.44880.0548-0.0048-0.03780.1067-0.0695-0.1302-0.03050.28870.01710.080.5160.02540.343222.040778.275285.5428
30.3036-0.27730.20460.69490.1020.3025-0.0159-0.0907-0.0658-0.02790.00490.20920.0276-0.1974-00.26940.00010.02840.35880.02670.299328.958276.239777.043
40.47940.15280.20070.7377-0.20680.1790.0189-0.11530.06490.1033-0.0059-0.1064-0.04810.0498-00.27760.01420.00370.3609-0.01640.246447.101786.09882.5776
50.10370.0749-0.13280.1149-0.01010.28060.2037-0.10920.2458-0.0677-0.2342-0.46490.0238-0.06540.00010.27080.0179-0.0340.2876-0.04030.323858.156693.041682.3725
60.3653-0.0412-0.19060.03290.02410.093-0.0092-0.22680.05870.23650.02650.01550.0365-0.0849-00.26240.01680.00580.3347-0.02370.271242.448288.589480.8385
70.14810.16570.19010.44820.15020.24450.0347-0.06290.1371-0.0104-0.0520.1013-0.0988-0.05710.00010.2560.0157-0.00550.3164-0.02960.302536.59492.451975.0859
80.66490.0547-0.05340.66480.17640.93230.0138-0.0419-0.26270.032-0.00370.08490.1834-0.1369-00.3148-0.032-0.00030.2710.02870.378538.588654.569467.6693
90.03710.0317-0.08770.0683-0.08480.2035-0.11710.3686-0.2209-0.2580.08470.08510.3529-0.2324-0.00160.3446-0.0388-0.00270.3161-0.02590.444536.376651.857957.6501
100.0903-0.0572-0.0450.49090.32830.4388-0.01790.0716-0.11820.02360.041-0.11580.07560.0259-00.3130.01980.00510.31960.02910.36951.485161.461366.441
110.12910.08780.11660.08940.09210.1125-0.17240.22110.00880.03330.0615-0.54870.316-0.2287-0.00720.24850.0083-0.01770.3306-0.00560.492268.22868.73770.9714
120.14750.0546-0.09630.0168-0.03460.06110.1660.0068-0.10250.0811-0.06490.0141-0.02840.03860.00030.32730.0014-0.04270.2890.04920.385955.965861.917277.5054
130.15480.31150.05880.62410.10110.0812-0.05470.0442-0.1787-0.0148-0.0485-0.1654-0.023-0.3407-00.27280.03320.00110.30320.02570.347150.616363.878566.5854
140.0646-0.03850.05240.0562-0.04860.0581-0.08980.0104-0.36080.168-0.0053-0.24040.05540.049-0.00210.27890.0392-0.00280.30420.01560.35352.199471.223280.3655
150.04560.047-0.02960.11530.05840.12250.0428-0.1402-0.22240.02630.0684-0.216-0.0994-0.11650.00050.2740.030.00820.34520.00250.364257.029575.29567.8454
160.1098-0.069-0.09330.05140.04140.0972-0.0206-0.2008-0.32360.0770.0797-0.03610.172-0.13910.00020.3131-0.04740.02040.38130.08520.342332.881160.16275.3451
170.3882-0.11350.01230.2758-0.40590.6488-0.10020.02550.078-0.08010.06280.1038-0.0786-0.19760.00020.28340.0023-0.0350.3293-0.02820.352224.9838101.3862.0114
180.83010.54-0.22780.3576-0.18930.312-0.0588-0.06870.2235-0.134-0.0050.3177-0.0655-0.2358-0.00030.29290.0418-0.08250.3685-0.03630.433119.4542100.356759.2051
190.2470.29330.59290.39610.58071.77240.0839-0.34550.18390.3389-0.18040.1510.4083-0.49310.01470.23660.0330.00530.3583-0.06240.467819.445395.505269.499
200.307-0.14840.08990.4314-0.03320.3957-0.0523-0.00320.1358-0.03990.02460.1024-0.1968-0.0253-00.32020.0287-0.03810.2864-0.01520.328736.0459103.282662.0215
210.10220.04010.04490.01680.02680.07980.2225-0.23570.1729-0.14920.18850.0851-0.18080.14690.00410.3686-0.02960.00980.2869-0.02020.287552.7183111.443760.4365
220.94890.0321-0.16230.29270.25230.2475-0.1015-0.01020.1319-0.0825-0.06780.0322-0.13540.0732-0.00040.3357-0.008-0.06370.2471-0.00670.314238.778105.925854.2308
230.3880.4649-0.17710.5344-0.18790.1761-0.2075-0.10360.1478-0.11430.13090.1495-0.1611-0.0687-0.00010.32940.0154-0.04990.27540.00990.306832.605899.119352.2609
240.9693-0.53070.1740.4330.22540.7129-0.09430.013-0.0704-0.3231-0.1029-0.0608-0.0263-0.0447-0.00130.4084-0.0399-0.01320.32340.03570.292331.64191.29533.6602
250.70870.26720.12390.926-0.13670.4768-0.08840.13010.1227-0.06880.06990.0674-0.04970.0915-00.3537-0.0419-0.00460.27340.02550.253333.818791.311434.6906
261.7340.24341.34210.08620.20391.2268-0.10960.1780.3727-0.0269-0.08990.09550.127-0.1485-0.09480.3207-0.14880.01220.3490.10490.278960.421897.565836.2466
270.1135-0.0585-0.16520.0810.01060.3426-0.0340.2485-0.03130.06170.0048-0.10110.1773-0.0556-0.00190.3921-0.04470.01710.32060.03850.261749.62190.582628.0636
280.5771-0.15620.45940.0949-0.12010.3569-0.10080.16560.0971-0.08380.0147-0.08070.1484-0.0153-0.00010.383-0.04820.01670.33880.02790.300542.735791.449438.1363
290.03530.0442-0.03640.0655-0.07350.0928-0.06410.2802-0.0004-0.1582-0.1748-0.24020.06610.26630.00010.4305-0.02840.07020.45180.00680.288952.74181.311131.5825
300.3511-0.2450.0820.167-0.08080.1179-0.14550.29110.0682-0.15640.0925-0.02070.00190.172600.384-0.06660.00510.3189-0.00060.233540.896282.627136.2277
310.5135-0.15480.4190.5892-0.39960.47450.1858-0.1075-0.4227-0.0857-0.14390.1177-0.05780.0131-0.00460.305-0.02730.00430.3124-0.06730.294939.387862.766738.3271
320.9068-0.20220.01170.1136-0.12620.21220.0967-0.0049-0.4125-0.299-0.0036-0.1987-0.0020.19470.01740.4457-0.0529-0.00890.2877-0.10420.343734.580955.49734.1328
330.2067-0.21780.26430.4379-0.40720.4107-0.05090.1016-0.1716-0.15180.0653-0.02470.19930.06870.00010.3827-0.03250.02840.3145-0.03710.295136.154865.298338.6438
340.3858-0.22490.18720.1523-0.07830.13170.09880.19520.21960.0580.04-0.6492-0.15650.46830.00060.48060.00930.12070.499-0.12460.612357.634162.895833.5357
350.1185-0.09460.18560.1206-0.17340.3007-0.0390.2766-0.2079-0.23970.0524-0.3420.01050.1844-0.00010.3189-0.01650.03880.3076-0.02110.324256.901373.261745.1496
360.4852-0.69430.58472.0211-1.01780.73440.13620.537-0.0318-0.5545-0.01250.12980.08090.39590.11660.3384-0.04740.15230.494-0.05680.454169.900371.310142.4848
370.075-0.0527-0.08140.104-0.03860.2271-0.07220.2440.1292-0.2971-0.072-0.79860.12890.40750.01750.33440.05040.06380.3766-0.0310.493559.772259.153942.5514
380.1911-0.06720.12810.27860.08690.7703-0.00560.1111-0.0958-0.16590.0059-0.05160.05210.0921-00.30910.00930.05280.3227-0.03070.330255.166267.000848.1359
390.7546-0.33250.41460.1465-0.18480.22950.2157-0.1712-0.6972-0.133-0.0241-0.07920.2912-0.23230.01960.4024-0.0404-0.03610.2637-0.03120.436335.404651.863345.5382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 33 )A6 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 60 )A34 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 108 )A61 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 147 )A109 - 147
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 162 )A148 - 162
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 191 )A163 - 191
7X-RAY DIFFRACTION7chain 'A' and (resid 192 through 235 )A192 - 235
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 78 )B6 - 78
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 92 )B79 - 92
10X-RAY DIFFRACTION10chain 'B' and (resid 93 through 147 )B93 - 147
11X-RAY DIFFRACTION11chain 'B' and (resid 148 through 162 )B148 - 162
12X-RAY DIFFRACTION12chain 'B' and (resid 163 through 174 )B163 - 174
13X-RAY DIFFRACTION13chain 'B' and (resid 175 through 191 )B175 - 191
14X-RAY DIFFRACTION14chain 'B' and (resid 192 through 203 )B192 - 203
15X-RAY DIFFRACTION15chain 'B' and (resid 204 through 216 )B204 - 216
16X-RAY DIFFRACTION16chain 'B' and (resid 217 through 235 )B217 - 235
17X-RAY DIFFRACTION17chain 'C' and (resid 6 through 33 )C6 - 33
18X-RAY DIFFRACTION18chain 'C' and (resid 34 through 78 )C34 - 78
19X-RAY DIFFRACTION19chain 'C' and (resid 79 through 92 )C79 - 92
20X-RAY DIFFRACTION20chain 'C' and (resid 93 through 147 )C93 - 147
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 162 )C148 - 162
22X-RAY DIFFRACTION22chain 'C' and (resid 163 through 203 )C163 - 203
23X-RAY DIFFRACTION23chain 'C' and (resid 204 through 235 )C204 - 235
24X-RAY DIFFRACTION24chain 'D' and (resid 6 through 33 )D6 - 33
25X-RAY DIFFRACTION25chain 'D' and (resid 34 through 147 )D34 - 147
26X-RAY DIFFRACTION26chain 'D' and (resid 148 through 162 )D148 - 162
27X-RAY DIFFRACTION27chain 'D' and (resid 163 through 174 )D163 - 174
28X-RAY DIFFRACTION28chain 'D' and (resid 175 through 191 )D175 - 191
29X-RAY DIFFRACTION29chain 'D' and (resid 192 through 203 )D192 - 203
30X-RAY DIFFRACTION30chain 'D' and (resid 204 through 235 )D204 - 235
31X-RAY DIFFRACTION31chain 'E' and (resid 9 through 33 )E9 - 33
32X-RAY DIFFRACTION32chain 'E' and (resid 34 through 60 )E34 - 60
33X-RAY DIFFRACTION33chain 'E' and (resid 61 through 108 )E61 - 108
34X-RAY DIFFRACTION34chain 'E' and (resid 109 through 130 )E109 - 130
35X-RAY DIFFRACTION35chain 'E' and (resid 131 through 147 )E131 - 147
36X-RAY DIFFRACTION36chain 'E' and (resid 148 through 162 )E148 - 162
37X-RAY DIFFRACTION37chain 'E' and (resid 163 through 174 )E163 - 174
38X-RAY DIFFRACTION38chain 'E' and (resid 175 through 219 )E175 - 219
39X-RAY DIFFRACTION39chain 'E' and (resid 220 through 235 )E220 - 235

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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

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