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

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Basic information

Entry
Database: PDB / ID: 6xub
TitleStructure of coproheme decarboxylase from Corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Coproheme decarboxylase / heme b biosynthesis / decarboxylation / ferredoxin like / actinobacterial
Function / homologyHeme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / harderoheme (III) / Uncharacterized protein / Chlorite dismutase
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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)139,75710
Polymers136,4455
Non-polymers3,3135
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint-55 kcal/mol
Surface area41180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.969, 123.382, 78.009
Angle α, β, γ (deg.)90.000, 98.710, 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) / Variant (production host): Tuner / References: UniProt: A0A2T1BSE4, UniProt: Q6NGV6*PLUS
#2: Chemical
ChemComp-VOV / harderoheme (III)


Mass: 662.513 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C35H34FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 33500, MgCl2

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Data collection

DiffractionMean temperature: 170 K / Ambient temp details: cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5645→48.1924 Å / Num. obs: 156754 / % possible obs: 98.02 % / Redundancy: 3.05 % / CC1/2: 0.996 / Net I/σ(I): 6.33
Reflection shellResolution: 1.5645→1.621 Å / Num. unique obs: 14679 / CC1/2: 0.223 / % possible all: 92.16

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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: 1.78→48.1891 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.39
RfactorNum. reflection% reflection
Rfree0.2272 5271 4.95 %
Rwork0.1737 --
obs0.1764 106562 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 376.04 Å2 / Biso mean: 44.0519 Å2 / Biso min: 18.6 Å2
Refinement stepCycle: final / Resolution: 1.78→48.1891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9310 0 385 737 10432
Biso mean--58.85 38.88 -
Num. residues----1142
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.78-1.80020.41031670.3728295186
1.8002-1.82140.37971570.3554326895
1.8214-1.84360.351580.3428337297
1.8436-1.8670.33171570.3255336897
1.867-1.89150.31081850.3032338899
1.8915-1.91740.31091530.2926343399
1.9174-1.94480.31042060.2647336499
1.9448-1.97390.28571660.24343599
1.9739-2.00470.29661640.2378342399
2.0047-2.03760.271850.2258341199
2.0376-2.07270.27241960.2156337299
2.0727-2.11040.27461750.20013439100
2.1104-2.1510.2521510.19263441100
2.151-2.19490.27961590.19023451100
2.1949-2.24260.25121920.1894341699
2.2426-2.29480.21062060.1852337599
2.2948-2.35220.26741750.1802339198
2.3522-2.41580.26261790.1709335598
2.4158-2.48690.231740.1704342399
2.4869-2.56710.2481960.1751338499
2.5671-2.65890.2121510.1693346999
2.6589-2.76530.23141720.1695340899
2.7653-2.89120.24971660.1737340499
2.8912-3.04360.24291760.1809340298
3.0436-3.23420.25431890.1746331397
3.2342-3.48390.2191890.159329796
3.4839-3.83430.20281660.1438339997
3.8343-4.38880.17232070.1192336198
4.3888-5.52820.15921720.1212337797
5.5282-48.18910.19471820.1643340197
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)
10.50530.1204-0.11680.9842-0.05560.1064-0.1479-0.09890.06190.10480.06510.1776-0.0367-0.25590.00150.27240.02230.03390.3160.01130.236731.986579.666681.8599
20.7736-0.4640.1841.20280.50550.326-0.0933-0.2002-0.10580.204-0.01820.355-0.0939-0.2228-0.01450.27170.01530.0770.37020.00590.332825.236480.101681.7713
30.0388-0.0321-0.04130.02410.06740.1957-0.03330.2225-0.34420.16330.03620.43510.3146-0.130.00040.2668-0.01750.07550.31010.03810.369627.848569.510780.3547
40.1552-0.34250.01880.77190.0182-0.0113-0.0734-0.19690.0143-0.00280.05010.1144-0.0564-0.148900.30580.00160.01080.34890.01850.288438.020279.579880.3276
50.03640.0473-0.04890.1041-0.00710.11790.0155-0.24460.22480.41080.0921-0.0579-0.2442-0.00920.00050.30290.05630.02640.3757-0.00930.228836.949588.292690.2822
60.09620.07820.00160.39890.0535-0.0226-0.0968-0.0437-0.21420.00720.069-0.09670.0469-0.0149-0.00290.21690.0238-0.01210.2941-0.00070.256949.775986.393974.9889
70.23040.2822-0.10560.334-0.14080.07440.1835-0.34620.41260.1084-0.0175-0.3805-0.1127-0.06690.00260.27580.0268-0.04180.3067-0.03070.307555.379794.984583.0706
8-0.01070.08420.00670.34740.0339-0.00470.0037-0.1114-0.05350.1996-0.08680.1351-0.0074-0.12260.00020.25760.0320.00120.304-0.0160.237941.662786.70980.3381
90.06960.0145-0.0260.08430.11590.15560.1212-0.1180.11920.02180.1095-0.0131-0.2294-0.0328-0.00060.31830.0222-0.00790.3438-0.01330.34541.2587100.213876.5328
100.3392-0.08280.23870.0755-0.02620.07580.0016-0.1709-0.07070.0209-0.02060.057-0.0877-0.006700.24040.00690.01860.2947-0.00210.30734.31289.55974.4471
110.64370.1778-0.08530.7820.12521.1429-0.0807-0.1038-0.266-0.0008-0.00420.15090.1886-0.10140.00010.2737-0.01090.01940.25810.02780.356937.92954.244865.9681
120.2836-0.1694-0.04340.60370.13780.2108-0.0097-0.0576-0.10860.09950.0187-0.07710.02680.0614-00.26130.01240.00790.29210.03150.312451.136961.64866.6574
130.06290.0735-0.07190.1246-0.0260.07510.07530.08230.15520.0416-0.0726-0.5735-0.089-0.16320.00570.33770.0240.0420.3420.00930.482768.013468.685871.1266
140.07770.0873-0.0580.0739-0.0640.04440.182-0.0165-0.0590.16770.1119-0.14530.14320.02580.00570.29470.0228-0.03920.27550.03580.337455.626461.983577.6746
150.13480.17150.13510.58030.18980.1242-0.01340.047-0.1968-0.01850.0037-0.047-0.2535-0.1376-0.00040.27010.01340.00350.28140.01230.326350.432963.947766.6984
160.0815-0.02280.0760.0671-0.02720.0515-0.2961-0.1675-0.51820.2220.0304-0.20320.04670.1197-0.00050.2870.02970.01070.29110.0090.317851.928971.418280.5034
170.4117-0.15890.02370.13360.23610.5045-0.0475-0.034-0.2160.11170.0425-0.14060.0619-0.021900.22760.01420.01660.26030.03790.280343.009866.820772.1723
180.5353-0.1099-0.03330.4058-0.61080.9633-0.06430.03720.0749-0.04240.07810.1867-0.1721-0.13590.00040.29480.0262-0.02930.31720.0050.388824.8109101.526261.8492
190.3160.0804-0.05010.2117-0.0070.67080.0350.02110.2639-0.2748-0.08250.4479-0.1102-0.3780.0340.28650.0673-0.10420.3778-0.04770.561614.4461102.448260.2828
200.56040.09290.06960.7804-0.11740.5213-0.03190.01290.0872-0.1368-0.01250.1464-0.1162-0.070500.2990.0358-0.01920.2636-0.02290.299330.9112100.923362.1892
210.27460.1197-0.08540.0541-0.04880.02530.1607-0.03750.1486-0.42730.0707-0.10530.0150.40920.03160.3953-0.0507-0.00370.2734-0.02740.301552.5686111.719560.5327
220.5473-0.04910.1280.20430.24490.3204-0.0181-0.02480.1122-0.2637-0.01810.1314-0.14560.04510.00010.3460.0001-0.0250.2386-0.01380.270737.3613106.042957.8048
230.06950.0418-0.19150.0588-0.11550.3845-0.00030.06390.116-0.1359-0.04690.0474-0.185-0.0975-00.3547-0.0009-0.00750.2830.01140.284945.2293102.823951.1068
241.264-0.2273-0.05550.04380.14341.57660.0646-0.04150.2589-0.5593-0.05330.3389-0.07640.12610.49850.37010.0643-0.19430.22020.01630.394920.128999.091749.3267
250.2744-0.1653-0.1370.23690.32640.5151-0.10620.15330.1219-0.47410.05970.19430.0743-0.1399-0.00120.46990.005-0.02320.28230.04990.347635.261897.103633.8335
260.86690.21040.28151.1684-0.16530.506-0.0310.08250.1726-0.05470.02620.2710.03050.017500.3916-0.02010.00990.26760.01380.290833.069790.464434.6786
270.09750.0394-0.09270.0367-0.00980.1123-0.13470.2877-0.0881-0.07880.0437-0.3478-0.09860.16190.00010.4816-0.10070.05950.35260.0490.35760.219498.082336.2233
280.0525-0.08220.08180.137-0.02730.2269-0.01510.14330.21930.03640.1472-0.07440.20340.13080.00150.4467-0.0230.0550.39570.03010.261749.276890.639627.9908
290.6432-0.32330.46230.1629-0.23730.30710.01690.04410.1715-0.16590.1031-0.132-0.18780.0227-0.00010.4023-0.02320.0470.26920.01060.275742.661991.682138.0513
300.01650.0146-0.05910.0078-0.04780.15590.10630.1161-0.1632-0.3232-0.1498-0.2430.08950.00140.00050.4455-0.02640.06710.3723-0.00440.236652.56381.200431.5714
310.3425-0.3630.0020.3549-0.15010.4354-0.14430.17460.0621-0.31230.0490.0425-0.04580.0313-0.00060.4011-0.0329-0.01660.2921-0.00160.242340.479382.574735.8371
320.4458-0.0890.63270.31970.04430.85980.08340.1099-0.2937-0.09640.05520.2206-0.04-0.35020.03350.4084-0.02830.02120.3507-0.01550.321435.297162.578341.3086
330.4733-0.1440.27960.1454-0.23120.2699-0.00270.1114-0.287-0.22530.059-0.06490.21580.00310.00290.4817-0.04310.0030.2935-0.08280.307636.836858.670137.7516
340.1379-0.04850.10550.1530.04070.0952-0.08830.05470.186-0.60220.11390.26970.19160.03610.00010.4648-0.0411-0.02540.3159-0.04070.320332.818567.346132.1322
350.4603-0.21450.2180.7521-0.22660.08490.01860.1499-0.1144-0.07020.0217-0.26920.13650.1652-00.44830.0360.03650.3814-0.06820.382948.239564.41136.7415
360.39620.03450.18550.02540.08470.3141-0.00610.127-0.1243-0.36720.0089-0.12410.11330.221-0.00240.357-0.00330.11070.3487-0.00890.338862.284572.682344.0961
370.33260.38170.20030.49020.39550.45720.00210.2192-0.0675-0.2851-0.0342-0.14150.03560.121-0.00010.35310.03460.07960.2955-0.0290.301754.502764.602342.2253
380.0615-0.0474-0.09220.03350.07130.12820.0781-0.11240.0675-0.0029-0.1648-0.0610.20280.098700.33390.01940.0480.3332-0.02250.365358.275759.752752.7007
390.01960.035-0.01060.0395-0.07910.1147-0.1840.0259-0.1790.00990.1843-0.1318-0.24890.07110.00010.2985-0.0220.06370.3144-0.0060.2958.939873.472951.1087
400.1871-0.1113-0.04520.0975-0.11840.30720.3326-0.0973-0.5173-0.0358-0.1495-0.15810.2203-0.177900.3991-0.0255-0.04170.2744-0.01990.412537.202554.295446.4567
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 78 )A34 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 92 )A79 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 118 )A93 - 118
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 130 )A119 - 130
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 147 )A131 - 147
7X-RAY DIFFRACTION7chain 'A' and (resid 148 through 165 )A148 - 165
8X-RAY DIFFRACTION8chain 'A' and (resid 166 through 191 )A166 - 191
9X-RAY DIFFRACTION9chain 'A' and (resid 192 through 203 )A192 - 203
10X-RAY DIFFRACTION10chain 'A' and (resid 204 through 235 )A204 - 235
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 92 )B6 - 92
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 147 )B93 - 147
13X-RAY DIFFRACTION13chain 'B' and (resid 148 through 162 )B148 - 162
14X-RAY DIFFRACTION14chain 'B' and (resid 163 through 174 )B163 - 174
15X-RAY DIFFRACTION15chain 'B' and (resid 175 through 191 )B175 - 191
16X-RAY DIFFRACTION16chain 'B' and (resid 192 through 203 )B192 - 203
17X-RAY DIFFRACTION17chain 'B' and (resid 204 through 235 )B204 - 235
18X-RAY DIFFRACTION18chain 'C' and (resid 6 through 33 )C6 - 33
19X-RAY DIFFRACTION19chain 'C' and (resid 34 through 60 )C34 - 60
20X-RAY DIFFRACTION20chain 'C' and (resid 61 through 147 )C61 - 147
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 162 )C148 - 162
22X-RAY DIFFRACTION22chain 'C' and (resid 163 through 191 )C163 - 191
23X-RAY DIFFRACTION23chain 'C' and (resid 192 through 216 )C192 - 216
24X-RAY DIFFRACTION24chain 'C' and (resid 217 through 235 )C217 - 235
25X-RAY DIFFRACTION25chain 'D' and (resid 8 through 24 )D8 - 24
26X-RAY DIFFRACTION26chain 'D' and (resid 25 through 147 )D25 - 147
27X-RAY DIFFRACTION27chain 'D' and (resid 148 through 162 )D148 - 162
28X-RAY DIFFRACTION28chain 'D' and (resid 163 through 174 )D163 - 174
29X-RAY DIFFRACTION29chain 'D' and (resid 175 through 191 )D175 - 191
30X-RAY DIFFRACTION30chain 'D' and (resid 192 through 203 )D192 - 203
31X-RAY DIFFRACTION31chain 'D' and (resid 204 through 235 )D204 - 235
32X-RAY DIFFRACTION32chain 'E' and (resid 13 through 33 )E13 - 33
33X-RAY DIFFRACTION33chain 'E' and (resid 34 through 78 )E34 - 78
34X-RAY DIFFRACTION34chain 'E' and (resid 79 through 92 )E79 - 92
35X-RAY DIFFRACTION35chain 'E' and (resid 93 through 130 )E93 - 130
36X-RAY DIFFRACTION36chain 'E' and (resid 131 through 162 )E131 - 162
37X-RAY DIFFRACTION37chain 'E' and (resid 163 through 191 )E163 - 191
38X-RAY DIFFRACTION38chain 'E' and (resid 192 through 203 )E192 - 203
39X-RAY DIFFRACTION39chain 'E' and (resid 204 through 216 )E204 - 216
40X-RAY DIFFRACTION40chain 'E' and (resid 217 through 235 )E217 - 235

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  • 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

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