[English] 日本語
Yorodumi
- PDB-6mjn: Crystal structure of an organic hydroperoxide resistance protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mjn
TitleCrystal structure of an organic hydroperoxide resistance protein OsmC, predicted redox protein, regulator of sulfide bond formation from Legionella pneumophila
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / NIAID / structural genomics / disulfide / active site cysteine / redox / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


response to oxidative stress
Similarity search - Function
Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta ...Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Organic hydroperoxide resistance protein / Organic hydroperoxide resistance protein OsmC, predicted redox protein, regulator of sulfide bond formation
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of an organic hydroperoxide resistance protein OsmC, predicted redox protein, regulator of sulfide bond formation from Legionella pneumophila
Authors: Edwards, T.E. / Delker, S.L. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1187
Polymers63,0124
Non-polymers1063
Water3,621201
1
A: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5774
Polymers31,5062
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-69 kcal/mol
Surface area12090 Å2
MethodPISA
2
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5413
Polymers31,5062
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-55 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.550, 51.400, 82.340
Angle α, β, γ (deg.)90.000, 110.090, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Organic hydroperoxide resistance protein


Mass: 15752.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_09130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F4M7, UniProt: Q5ZU37*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: LepnA.00074.a.B1.PS38428 at 20.78 mg/mL against MCSG1 screen condition C4: 0.17 M ammonium acetate, 0.085 M sodium acetate pH 4.6, 25.5% PEG 4000, 15% ethylene glycol, crystal tracking ID ...Details: LepnA.00074.a.B1.PS38428 at 20.78 mg/mL against MCSG1 screen condition C4: 0.17 M ammonium acetate, 0.085 M sodium acetate pH 4.6, 25.5% PEG 4000, 15% ethylene glycol, crystal tracking ID 300656c4, unique puck ID zem2-15

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.75→42.806 Å / Num. obs: 59868 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 43.206 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.04 / Χ2: 1.069 / Net I/σ(I): 15.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.83.4490.4352.5444720.9240.51799.7
1.8-1.843.4160.3223.3643590.9490.38499.9
1.84-1.93.3680.2394.542480.9720.28599.9
1.9-1.963.2370.1596.3341030.9860.19199.7
1.96-2.023.2740.1228.0440270.990.14799.8
2.02-2.093.4860.09610.3938300.9930.11499.7
2.09-2.173.420.0812.4737470.9950.09699.4
2.17-2.263.3430.06614.7935650.9950.07999
2.26-2.363.1590.05616.6434180.9960.06798.8
2.36-2.473.2270.0518.9132550.9970.0698.5
2.47-2.613.3810.04421.8530630.9970.05397.2
2.61-2.773.2960.0423.9428710.9970.04896.4
2.77-2.963.1430.03725.727080.9970.04596
2.96-3.23.0310.03626.9325180.9970.04395.8
3.2-3.53.3150.03230.2422690.9980.03894.1
3.5-3.913.280.03130.920350.9980.03692.8
3.91-4.523.0280.0330.0218520.9980.03696
4.52-5.533.240.02831.3215900.9980.03395.5
5.53-7.833.2270.02631.2812270.9990.03194.8
7.83-42.8063.1140.02430.967110.9980.02995.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EER
Resolution: 1.75→42.806 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.78
RfactorNum. reflection% reflection
Rfree0.2093 3432 6.06 %
Rwork0.1812 --
obs0.183 56617 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.83 Å2 / Biso mean: 53.5157 Å2 / Biso min: 20.4 Å2
Refinement stepCycle: final / Resolution: 1.75→42.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 3 203 4106
Biso mean--64.68 51.6 -
Num. residues----554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.7740.35911150.34451850196580
1.774-1.79930.37091040.32061832193682
1.7993-1.82620.34641210.29141936205784
1.8262-1.85470.32511140.2811917203185
1.8547-1.88510.30361220.26771955207785
1.8851-1.91760.28411240.24352002212688
1.9176-1.95250.28651540.24472051220591
1.9525-1.990.25791420.22912109225192
1.99-2.03070.23981300.21732175230595
2.0307-2.07480.20591490.22442162231196
2.0748-2.12310.27021260.20742233235997
2.1231-2.17620.23651430.20442204234797
2.1762-2.2350.22821290.19542246237597
2.235-2.30080.21491250.19072229235497
2.3008-2.3750.21931340.19222225235997
2.375-2.45990.24811660.19682230239697
2.4599-2.55840.20861500.19662213236397
2.5584-2.67480.2221590.18962158231796
2.6748-2.81580.22861480.18572189233796
2.8158-2.99220.2491670.19382197236496
2.9922-3.22310.20921500.18382199234996
3.2231-3.54730.18641390.16532151229094
3.5473-4.06030.17161390.15172175231494
4.0603-5.11420.15261420.14182262240496
5.1142-42.81910.20981400.17382285242595
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)
15.46250.20810.84464.05920.7717.03980.01040.03760.2377-0.1733-0.02230.6566-0.0165-0.74020.04280.2327-0.0011-0.020.2825-0.0490.3885-4.63121.112928.3912
27.20360.8208-1.033.7813-0.23436.2559-0.26291.17510.0534-0.74350.08810.3266-0.3349-0.07030.03280.41610.0387-0.10330.43290.12080.36473.7139.785416.1301
34.8370.81383.74781.14030.77366.77460.2979-0.50620.32280.1251-0.09410.11610.149-0.4695-0.00810.2951-0.01180.03360.2214-0.03230.307112.08715.799937.3641
44.4329-0.5149-0.44194.15070.55458.26890.17970.0380.03760.001-0.188-0.07950.1497-0.20990.0270.2165-0.03830.00910.18510.00530.327217.66956.388132.3027
55.23640.60563.5953.50722.72917.7389-0.15380.19920.4149-0.369-0.23150.2614-0.5762-0.07660.56770.2356-0.03390.04340.17760.01530.29820.37188.209633.3843
65.03751.41511.50560.4736-0.2255.55590.2971-0.0078-0.46810.36550.0218-0.37950.48640.1706-0.26340.3210.0639-0.00970.2299-0.02980.334324.22564.495243.1144
76.23374.32322.51492.89462.40643.61010.23270.0953-0.20820.2512-0.0384-0.31760.21250.1618-0.19020.28720.04-0.02350.1353-0.01720.289818.88310.832334.3469
85.797-2.171-1.42842.5631.17518.09870.1440.21010.5287-0.1959-0.0733-0.1225-0.2350.118-0.2110.2753-0.0401-0.01950.20230.05070.344714.058910.190227.258
95.11250.8589-1.04764.5874-5.57618.05730.19660.15350.9789-0.31560.18270.5466-0.9878-0.2464-0.38260.40.0369-0.02550.19860.01170.46657.164915.638528.0906
107.27972.0346-0.46867.5203-3.65818.12810.2554-0.96740.73930.8329-0.23890.7609-0.4991-0.6374-0.16580.32490.04490.1060.3655-0.09110.4161-0.8017.922340.2851
113.45120.57090.33066.82835.50393.9591-0.06460.55680.2214-0.47150.18690.0603-0.3811-0.1601-0.12240.2547-0.0454-0.00590.32030.03270.27222.5535-3.065620.794
121.91340.954-4.04673.6258-1.20348.7981-0.05733.8659-1.3052-1.7524-0.02970.6892-0.1496-0.69820.61850.5764-0.1576-0.03730.8578-0.24880.47-4.1452-10.31036.6221
136.83691.81892.76384.32962.63727.3471-0.1386-0.2243-0.26230.22840.1533-0.01040.12270.19840.03830.2661-0.0160.02580.21430.01440.31082.5644-6.822133.7792
147.45972.38544.49713.90993.77374.1855-0.1412-0.65160.2822-0.2214-0.37610.3518-0.1801-1.3630.48460.2077-0.0211-0.02170.22880.00380.267-2.3686-9.916324.5181
155.88564.10325.75319.27236.19226.39420.04420.4078-1.2014-0.11060.4596-0.85940.35460.7572-0.52450.34610.0325-0.02130.3537-0.0030.31250.577-15.933515.905
164.5369-4.91193.25385.8689-2.37898.44920.0590.2158-0.5041-0.40530.41630.03590.6529-0.1483-0.49680.2746-0.039-0.00870.2788-0.01160.313110.9143-8.796925.3749
174.68095.95954.39857.88726.10064.8483-0.32130.439-0.1773-0.20030.16970.0955-0.1917-0.28670.24940.4074-0.0652-0.02010.4308-0.0090.3945-4.6646-13.91221.9922
186.49371.65044.47714.23061.71713.235-0.4220.7128-1.38810.91970.5948-0.36560.99020.34210.30440.5944-0.04360.30660.8621-0.38950.251524.6493-6.7427-22.2333
194.89193.74951.015.77144.38734.72960.5408-1.0309-1.09991.2012-0.9227-1.2686-0.9208-0.1031-0.40091.25540.28860.05830.55540.27430.756126.9511-13.4516-1.7851
202.0848-0.2801-0.50472.96532.4332.0318-0.0937-0.0463-1.13670.51840.797-1.35280.92851.03021.25511.14250.82280.20060.6449-0.17690.802732.6559-12.1641-10.7831
215.0355-1.6487-0.20237.91151.49732.05030.3155-0.5649-0.88870.7305-0.65940.57340.8180.5997-0.2841.02350.8628-0.04711.00310.17410.563630.1374-6.04393.7195
224.5641-0.95381.15729.3541-2.44913.0335-0.3238-0.4090.0823-0.51190.2223-0.58960.7251.00770.23520.27860.08190.01220.5666-0.05940.295929.57225.7029-10.9595
239.24551.9219-3.75223.649-1.26045.6088-0.5886-0.7244-0.0552-0.29050.2909-0.17670.63260.77350.37990.3690.0329-0.00110.4521-0.10640.233625.53319.3184-5.5979
248.11043.2061-2.99046.0086-2.75846.81690.2784-1.02920.94710.3391-0.3199-0.2421-1.06421.3282-0.05930.3355-0.0732-0.03390.5605-0.14920.417929.004716.0468-8.8392
252.2266-0.4834-0.55133.05193.2143.32430.06240.37271.1001-0.66190.4684-0.2727-1.09460.038-0.47330.5839-0.05490.01020.4484-0.03410.640525.258919.8988-16.5697
263.61694.3573-3.04657.7312-0.08939.0065-0.3075-0.26210.8945-0.2640.46560.1449-0.23190.0588-0.14330.29430.0216-0.02820.33830.04850.292817.92577.1894-11.636
272.25352.1901-2.33242.1435-2.0517.68970.308-0.66271.3634-0.31790.2873-0.0184-1.48661.5222-0.12330.5211-0.14930.1160.6506-0.15910.604527.321619.0344-8.1976
287.5422-2.4183-3.68423.62390.33738.8186-0.2279-1.0670.14210.09180.4005-0.19820.52021.246-0.14080.37560.0509-0.07860.6802-0.14390.376629.98466.9633-2.9867
297.69442.63960.59144.67241.89233.473-0.1603-0.1168-1.07810.26960.4057-0.53170.90871.09920.00970.58010.26680.01010.6220.01710.470129.2799-4.2008-9.1705
308.61742.4856-2.42292.05650.06166.1895-0.2248-0.2283-0.9980.31160.01320.14481.1905-0.29920.00820.8725-0.05880.16330.32860.03830.564115.8381-11.535-10.0463
319.55251.1309-1.7878.3238-2.07422.1472-0.1793-0.7738-0.64730.59290.14610.59770.9508-0.19570.16710.44450.07620.07880.39780.06940.335513.1221-1.4794-7.3401
320.791-1.8541.69334.2669-3.88143.48130.6286-0.1328-1.05120.1166-0.2577-0.83750.6528-0.4378-0.57711.1844-0.17620.36080.4764-0.01731.245713.1547-16.33-10.6745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )A2 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 44 )A27 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 67 )A45 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 90 )A68 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 105 )A91 - 105
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 119 )A106 - 119
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 139 )A120 - 139
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 16 )B0 - 16
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 26 )B17 - 26
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 44 )B27 - 44
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 67 )B45 - 67
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 73 )B68 - 73
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 90 )B74 - 90
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 105 )B91 - 105
15X-RAY DIFFRACTION15chain 'B' and (resid 106 through 118 )B106 - 118
16X-RAY DIFFRACTION16chain 'B' and (resid 119 through 131 )B119 - 131
17X-RAY DIFFRACTION17chain 'B' and (resid 132 through 139 )B132 - 139
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 8 )C2 - 8
19X-RAY DIFFRACTION19chain 'C' and (resid 9 through 16 )C9 - 16
20X-RAY DIFFRACTION20chain 'C' and (resid 17 through 26 )C17 - 26
21X-RAY DIFFRACTION21chain 'C' and (resid 27 through 36 )C27 - 36
22X-RAY DIFFRACTION22chain 'C' and (resid 37 through 68 )C37 - 68
23X-RAY DIFFRACTION23chain 'C' and (resid 69 through 91 )C69 - 91
24X-RAY DIFFRACTION24chain 'C' and (resid 92 through 105 )C92 - 105
25X-RAY DIFFRACTION25chain 'C' and (resid 106 through 119 )C106 - 119
26X-RAY DIFFRACTION26chain 'C' and (resid 120 through 131 )C120 - 131
27X-RAY DIFFRACTION27chain 'C' and (resid 132 through 138 )C132 - 138
28X-RAY DIFFRACTION28chain 'D' and (resid 0 through 17 )D0 - 17
29X-RAY DIFFRACTION29chain 'D' and (resid 18 through 67 )D18 - 67
30X-RAY DIFFRACTION30chain 'D' and (resid 68 through 117 )D68 - 117
31X-RAY DIFFRACTION31chain 'D' and (resid 118 through 131 )D118 - 131
32X-RAY DIFFRACTION32chain 'D' and (resid 132 through 138 )D132 - 138

+
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://pdbjlvh1.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