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- PDB-7s5o: Crystal structure of Cytochrome c' beta from Nitrosomonas europae... -

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Basic information

Entry
Database: PDB / ID: 7s5o
TitleCrystal structure of Cytochrome c' beta from Nitrosomonas europaea ATCC 19718
ComponentsCytochrome_P460 domain-containing protein
KeywordsMETAL BINDING PROTEIN / SSGCID / Cytochrome_P460 domain-containing protein / Nitrosomonas europaea / NE0824 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / ACETATE ION / HEME C / Cytochrome_P460 domain-containing protein
Function and homology information
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: Biochemistry / Year: 2022
Title: Structural Characterization of Cytochrome c ' beta-Met from an Ammonia-Oxidizing Bacterium.
Authors: Abendroth, J. / Buchko, G.W. / Liew, F.N. / Nguyen, J.N. / Kim, H.J.
History
DepositionSep 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome_P460 domain-containing protein
B: Cytochrome_P460 domain-containing protein
C: Cytochrome_P460 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,77215
Polymers57,1633
Non-polymers2,60912
Water10,755597
1
A: Cytochrome_P460 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9245
Polymers19,0541
Non-polymers8704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome_P460 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8284
Polymers19,0541
Non-polymers7743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome_P460 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0206
Polymers19,0541
Non-polymers9665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.790, 88.170, 75.850
Angle α, β, γ (deg.)90.000, 101.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome_P460 domain-containing protein / NieuA.20425.a.K12


Mass: 19054.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298) (bacteria)
Strain: ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298 / Gene: NE0824 / Plasmid: NieuA.20425.a.K12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82W71
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.4 Å3/Da / Density % sol: 48.9 % / Mosaicity: 0.123 °
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.77
Details: Calibre Anatrace Top96 screen, condition #30 optimization screen: 100mM sodium acetate HCl pH 4.77, 2245mM ammonium sulfate) + 100mM sodium malonate pH 7.0; NieuA.20425.a.K12.PB00109 at ...Details: Calibre Anatrace Top96 screen, condition #30 optimization screen: 100mM sodium acetate HCl pH 4.77, 2245mM ammonium sulfate) + 100mM sodium malonate pH 7.0; NieuA.20425.a.K12.PB00109 at 10mg/ml, tray: 319288 F8; cryo: 7ul reservoir + 14ul 4M ammonium sulfate, 60sec soak; puck hyq3-1, For phasing: Anatrace Top96 screen, optimization screen around condition #30: 100mM Sodium acetate / HCl pH 5.0, 2245mM ammonium sulfate NieuA.20425.a.K12.PB00109 at 10mg/ml; tray: 318611 h8; puck rwi1-1. 3x 360deg were collected at the in-house system at Cu-Kalpha, 1.5418A

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDateDetails
RAYONIX MX-3001CCDMar 11, 2021Beryllium Lenses
RIGAKU SATURN 944+2CCDJan 6, 2021
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond [111]SINGLE WAVELENGTHMx-ray1
2RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.8→50 Å / Num. obs: 48663 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.083 / Χ2: 0.955 / Net I/σ(I): 14.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.853.10.3552.9129680.8650.42980.4
1.85-1.93.350.3273.5332160.8930.38989.7
1.9-1.953.910.2764.833230.9410.31996.2
1.95-2.014.790.2426.334070.9650.27299.8
2.01-2.085.270.2137.832880.9740.237100
2.08-2.155.280.1769.2431390.9820.195100
2.15-2.235.270.14910.7330870.9860.16699.9
2.23-2.325.240.12612.1629850.9880.1499.9
2.32-2.435.290.11413.3727970.9910.126100
2.43-2.555.260.10214.8626950.9930.11399.8
2.55-2.685.260.0916.5525910.9940.1100
2.68-2.855.240.07718.8424330.9950.08699.8
2.85-3.045.220.06821.4823190.9960.076100
3.04-3.295.170.05624.7621250.9970.06299.9
3.29-3.65.140.04728.3319720.9980.052100
3.6-4.025.10.04131.5817860.9980.04699.9
4.02-4.655.120.03733.9315860.9980.04199.9
4.65-5.695.150.03833.6513210.9980.04299.9
5.69-8.055.010.0432.5710500.9980.044100
8.05-504.720.03135.045750.9990.03498.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
CRANK2phasing
Cootmodel building
SHELXDphasing
PARROTphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.94 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 2095 4.31 %0
Rwork0.1546 46557 --
obs0.1561 48652 97.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.94 Å2 / Biso mean: 22.8387 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.8→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 171 612 4415
Biso mean--19.31 30.98 -
Num. residues----472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.24551020.20852524262680
1.84-1.890.24651500.19472790294089
1.89-1.940.26111270.18333011313895
1.94-20.20021520.166731683320100
2-2.060.19851490.154931373286100
2.06-2.130.20321480.149131653313100
2.13-2.220.16951400.151531983338100
2.22-2.320.19011290.153132203349100
2.32-2.440.21571530.15331363289100
2.44-2.60.19121360.16231883324100
2.6-2.80.20111560.159331813337100
2.8-3.080.18321380.160831703308100
3.08-3.520.17211390.151931993338100
3.52-4.440.14921370.123532273364100
4.44-35.940.19791390.159732433382100
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)
17.28811.209-0.19063.6904-0.03983.5859-0.02220.9184-0.3568-0.41750.0796-0.15180.19970.1363-0.01010.24110.01960.02050.2305-0.00390.09954.5190.82748.602
21.9657-0.5404-0.33591.7539-0.33511.5194-0.00570.0959-0.1256-0.0451-0.02430.21610.0972-0.25550.05260.0921-0.0118-0.02060.1505-0.03590.1182-9.3454.11158.783
34.9776-3.8286-0.65736.5782-5.08479.4518-0.0048-0.093-0.4207-0.10370.2481-0.13950.2811-0.2504-0.22750.1623-0.03760.02310.0967-0.00190.2461-3.14-11.05564.376
41.9244-2.46210.30615.7984-2.1362.8253-0.1462-0.0306-0.01280.3688-0.04670.06160.0424-0.16830.19440.1181-0.0126-0.01510.0874-0.03980.1192-2.435-0.97459.987
56.2072-1.1535-0.19394.73071.12347.2960.11470.41280.6479-0.9082-0.02970.6231-1.2595-0.7223-0.06230.35190.1237-0.070.31080.00990.2886-16.5122.30355.261
67.4701-0.8163-0.47354.28390.85940.32970.0516-0.1509-0.3232-0.0527-0.12150.4277-0.2623-0.71070.08780.13630.0571-0.0440.2909-0.05370.247-19.11513.9459.864
72.7869-0.002-0.2242.24520.07912.52310.03410.1286-0.0573-0.2592-0.1667-0.35670.24570.23760.10320.1220.01850.03070.1007-0.01640.12415.725-0.49954.614
84.1107-1.09861.27854.0862-2.00586.7346-0.0979-0.0081-0.10140.1723-0.0685-0.4058-0.14470.57080.14940.11560.01160.00780.121-0.0060.13798.8022.07657.933
94.15031.40151.59154.09891.60465.4779-0.13450.47210.3611-0.3439-0.10890.0289-0.74910.13640.20860.20380.0068-0.00670.16150.03360.12772.11110.86348.776
103.77460.4035-0.84634.018-1.1145.3989-0.0332-0.1922-0.08730.1972-0.0504-0.2717-0.12230.26650.06010.1156-0.0043-0.01540.0876-0.01880.10694.5944.40667.371
118.28234.3872.05755.78170.4847.53180.0789-0.3296-0.5020.12470.02370.45620.6056-0.7549-0.10070.1534-0.04770.0230.19750.01620.2557-10.09-5.52368.275
122.52661.67260.46344.39781.13834.17690.0964-0.24650.5490.6717-0.13240.2565-0.3859-0.30470.10590.22720.01660.03690.1335-0.04710.1794-3.14925.03886.131
133.4913-0.5379-1.06892.6066-1.34471.2169-0.0468-0.37320.14790.38410.0619-0.2355-0.21220.4531-0.01790.1679-0.0203-0.03460.1396-0.01360.140312.43619.91982.587
142.01790.0235-0.5611.9994-1.47432.19970.0790.14560.0581-0.06150.0153-0.0683-0.0629-0.0297-0.02550.1123-0.00770.01280.0716-0.01550.11448.88719.74673.246
152.2547-0.4882-1.7988.0356-2.00955.74350.0622-0.00040.04090.5982-0.2358-0.4565-0.04470.1590.15030.1435-0.0093-0.03290.18560.00540.10728.6478.41990.383
161.50730.3897-0.7534.0553-3.54464.1762-0.0244-0.122-0.0186-0.03560.0318-0.04250.20690.0771-0.11270.1498-0.00420.00610.0917-0.01660.09225.05615.50182.394
173.3345-0.4377-0.00314.9291-2.78749.32040.03690.91620.7033-0.2971-0.102-0.0473-0.34570.3257-0.01060.1901-0.00340.0460.23140.08690.231213.20829.5159.575
182.31150.0028-0.80952.3460.04132.24070.15640.03760.203-0.0153-0.0398-0.1854-0.20540.1383-0.07110.10980.0008-0.01150.088-0.02390.090910.59623.31473.303
191.6239-0.2151-0.22892.28660.10741.6792-0.1632-1.0753-0.41050.67360.29410.7190.2396-0.70240.0440.22070.03020.12190.38780.07990.2724-10.51615.23489.784
203.64860.4112-0.43634.4842-0.38372.5015-0.0129-0.2305-0.13740.2595-0.03240.5402-0.0054-0.23690.03460.10820.01640.02510.1499-0.01320.1414-6.43916.60281.604
212.58920.3317-0.04043.54220.89881.9037-0.42070.03890.6409-0.8261-0.14150.6525-0.8924-0.2971-0.0460.21710.0577-0.07180.1509-0.03420.2636-2.79929.26776.638
223.4033-0.9687-0.24233.74870.2932.517-0.0454-0.0281-0.2309-0.1778-0.05990.32320.1061-0.20270.05830.1213-0.0141-0.01580.1203-0.02020.1023-1.6219.03175.697
238.34281.74084.05188.1744-1.61792.86190.0212-0.4138-0.18660.3850.0112-0.7680.35250.2235-0.0730.16810.0448-0.01870.188-0.02950.199514.4227.83582.533
244.1211-0.4696-0.36532.64351.05062.97120.03210.01670.03720.0208-0.0555-0.0107-0.0911-0.14310.02010.1492-0.01410.00660.1213-0.00190.05313.7670.015100.718
256.0739-1.71451.69173.49451.4943.2603-0.0466-1.02280.24040.7111-0.0084-0.03480.20280.0080.04060.2277-0.0432-0.00830.2747-0.02940.13115.285.322116.357
262.0836-1.9675-2.09374.44863.29464.6566-0.02550.1291-0.144-0.03620.0755-0.21110.20610.1245-0.00870.1381-0.0107-0.00250.1715-0.02250.149511.593-9.47291.587
275.0974-0.7439-3.30881.07380.23192.60930.1399-0.02530.0040.0615-0.20710.2129-0.2137-0.41970.02990.1424-0.00310.02360.1917-0.04160.1355-5.6251.203106.085
283.33330.7707-0.4962.7824-0.82141.91360.0671-0.2157-0.20410.0192-0.01060.2190.523-0.4804-0.06140.1969-0.05940.02250.1664-0.03610.1656-3.8-5.703105.711
296.99651.83431.08572.80710.98034.8312-0.12360.05450.64250.132-0.1128-0.1983-0.43160.37220.15480.1805-0.0176-0.05950.22480.01860.175114.4453.316112.34
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 22:33 )A22 - 33
2X-RAY DIFFRACTION2( CHAIN A AND RESID 34:58 )A34 - 58
3X-RAY DIFFRACTION3( CHAIN A AND RESID 59:67 )A59 - 67
4X-RAY DIFFRACTION4( CHAIN A AND RESID 68:83 )A68 - 83
5X-RAY DIFFRACTION5( CHAIN A AND RESID 84:93 )A84 - 93
6X-RAY DIFFRACTION6( CHAIN A AND RESID 94:103 )A94 - 103
7X-RAY DIFFRACTION7( CHAIN A AND RESID 104:122 )A104 - 122
8X-RAY DIFFRACTION8( CHAIN A AND RESID 123:135 )A123 - 135
9X-RAY DIFFRACTION9( CHAIN A AND RESID 136:147 )A136 - 147
10X-RAY DIFFRACTION10( CHAIN A AND RESID 148:163 )A148 - 163
11X-RAY DIFFRACTION11( CHAIN A AND RESID 164:176 )A164 - 176
12X-RAY DIFFRACTION12( CHAIN B AND RESID 22:33 )B22 - 33
13X-RAY DIFFRACTION13( CHAIN B AND RESID 34:45 )B34 - 45
14X-RAY DIFFRACTION14( CHAIN B AND RESID 46:58 )B46 - 58
15X-RAY DIFFRACTION15( CHAIN B AND RESID 59:67 )B59 - 67
16X-RAY DIFFRACTION16( CHAIN B AND RESID 68:83 )B68 - 83
17X-RAY DIFFRACTION17( CHAIN B AND RESID 84:93 )B84 - 93
18X-RAY DIFFRACTION18( CHAIN B AND RESID 94:113 )B94 - 113
19X-RAY DIFFRACTION19( CHAIN B AND RESID 114:122 )B114 - 122
20X-RAY DIFFRACTION20( CHAIN B AND RESID 123:135 )B123 - 135
21X-RAY DIFFRACTION21( CHAIN B AND RESID 136:147 )B136 - 147
22X-RAY DIFFRACTION22( CHAIN B AND RESID 148:163 )B148 - 163
23X-RAY DIFFRACTION23( CHAIN B AND RESID 164:176 )B164 - 176
24X-RAY DIFFRACTION24( CHAIN C AND RESID 0:58 )C0 - 58
25X-RAY DIFFRACTION25( CHAIN C AND RESID 59:75 )C59 - 75
26X-RAY DIFFRACTION26( CHAIN C AND RESID 76:103 )C76 - 103
27X-RAY DIFFRACTION27( CHAIN C AND RESID 104:122 )C104 - 122
28X-RAY DIFFRACTION28( CHAIN C AND RESID 123:163 )C123 - 163
29X-RAY DIFFRACTION29( CHAIN C AND RESID 164:180 )C164 - 180

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