[English] 日本語
Yorodumi
- PDB-8cj4: Crystal structure of ClpP from Staphylococcus epidermidis, tetrad... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cj4
TitleCrystal structure of ClpP from Staphylococcus epidermidis, tetradecamer
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Serine protease / apo protein / ClpP
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlves Franca, B. / Rohde, H. / Betzel, C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)390715994 Germany
German Federal Ministry for Education and Research05K16GUA Germany
German Federal Ministry for Education and Research5K19GU4 Germany
CitationJournal: Sci Rep / Year: 2024
Title: Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds.
Authors: Alves Franca, B. / Falke, S. / Rohde, H. / Betzel, C.
History
DepositionFeb 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,13928
Polymers309,48414
Non-polymers1,65414
Water29,5631641
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SEC-SAXS results indicate that the structure is a tetradecamer (approx. 300kDa)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55250 Å2
ΔGint-401 kcal/mol
Surface area85900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.423, 123.662, 126.787
Angle α, β, γ (deg.)90.00, 91.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 22106.025 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria)
Gene: clpP, E1M97_03460, E1M98_06460, E1N00_07180, E1N03_05195, E1N04_00635, E1N05_04945, E1N06_06240, E1N09_07235, E1N11_03825, E1N12_01760, E1N13_04220, FHG76_01330, FHQ17_10195, H3963_07430, I3V53_07130
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A0N1MQL5, endopeptidase Clp
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1641 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate (pH 4.5), 35% v/v MPD and 40mM calcium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→44.96 Å / Num. obs: 227961 / % possible obs: 98.65 % / Redundancy: 7 % / Biso Wilson estimate: 27.82 Å2 / CC1/2: 1 / Rrim(I) all: 0.09 / Net I/σ(I): 14.12
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 22466 / CC1/2: 0.8 / Rrim(I) all: 0.94 / % possible all: 97.58

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.96 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 2392 1.05 %
Rwork0.1825 --
obs0.1829 227921 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19366 0 112 1641 21119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.949
X-RAY DIFFRACTIONf_dihedral_angle_d7.3762752
X-RAY DIFFRACTIONf_chiral_restr0.0593116
X-RAY DIFFRACTIONf_plane_restr0.013492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.28821380.252313038X-RAY DIFFRACTION97
1.94-1.980.26811400.242213140X-RAY DIFFRACTION98
1.98-2.030.30561390.224613106X-RAY DIFFRACTION98
2.03-2.080.28471390.209613102X-RAY DIFFRACTION98
2.08-2.130.24141400.198813181X-RAY DIFFRACTION98
2.13-2.20.22891390.191513134X-RAY DIFFRACTION98
2.2-2.270.23631410.181413222X-RAY DIFFRACTION98
2.27-2.350.20981400.179713208X-RAY DIFFRACTION99
2.35-2.440.21111400.182413250X-RAY DIFFRACTION99
2.44-2.550.21391410.181513251X-RAY DIFFRACTION99
2.55-2.690.23661410.182313313X-RAY DIFFRACTION99
2.69-2.860.19711410.185513312X-RAY DIFFRACTION99
2.86-3.080.21841420.189713372X-RAY DIFFRACTION99
3.08-3.390.27031420.191513362X-RAY DIFFRACTION100
3.39-3.880.211420.172213388X-RAY DIFFRACTION99
3.88-4.880.17961440.152213512X-RAY DIFFRACTION100
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)
10.06550.02070.0665-0.01120.00790.0111-0.0918-0.5298-0.56160.17010.0210.01740.40090.2817-0.00020.5110.0330.0980.40420.09440.322-35.9264-50.47742.4293
20.3311-0.44970.11980.5130.0298-0.0244-0.0060.0193-0.10690.1117-0.0302-0.00620.2346-0.06890.13890.4204-0.04630.18250.32530.05420.3272-46.3958-46.828-5.0534
30.4972-0.56940.10690.5546-0.0610.7345-0.2385-0.07840.00060.0674-0.14220.22390.2003-0.1644-1.2060.2931-0.08380.19610.32150.03590.2816-52.3159-37.4405-8.1301
40.3174-0.05850.14790.5431-0.04120.1001-0.07920.07940.0239-0.0459-0.09460.41440.1775-0.398-0.06860.1917-0.05390.07480.3208-0.00650.3892-59.7999-34.3358-21.9719
50.90710.06680.18920.36050.21840.5091-0.1601-0.13920.26120.2439-0.01350.3135-0.062-0.2677-0.29830.2956-0.00990.16340.37270.00620.3724-57.4549-26.8267-4.4358
60.0146-0.0364-0.00420.002-0.0226-0.0376-0.14580.0359-0.53140.05480.00080.29930.2940.10350.00020.42880.01740.01810.31280.05750.3838-21.4202-48.72956.0576
70.4154-0.31520.09980.72010.11550.2864-0.0636-0.123-0.16470.18370.0470.15160.1318-0.0648-0.15820.36840.03290.1030.3030.09460.212-32.6032-35.37267.2436
80.06930.07620.26680.47150.23610.1044-0.11990.04060.08360.1112-0.03070.05530.04480.0674-00.30820.06790.05260.31640.06680.2404-29.1986-22.33723.5689
90.0154-0.29650.08190.10010.13610.233-0.1648-0.1610.02280.12320.04260.27580.1011-0.3289-0.02740.26480.01880.10050.33590.04370.3176-42.2641-16.5251-1.3438
100.16360.14480.04090.31830.19610.1086-0.1009-0.11070.37170.3020.04240.1222-0.11070.0005-0.00040.38510.07770.06310.34240.05060.2943-28.3247-12.3797.4221
110.0601-0.11880.0610.2685-0.10830.1263-0.1278-0.5937-0.31070.46030.31960.19410.23660.06140.07260.59820.17770.00590.42680.04230.1925-21.2651-24.30616.9541
120.0221-0.1427-0.07480.07430.10440.02920.10750.0881-0.21490.06750.0370.37180.82910.09570.00010.40740.02460.00250.30330.03020.303-10.1279-53.97850.5766
130.9339-0.3005-0.1330.9716-0.31920.2356-0.05260.0071-0.07040.07470.08130.08230.02270.02280.00010.28170.0308-0.02650.22470.03930.1796-8.408-36.71415.0146
140.1079-0.19050.12540.0361-0.1309-0.1808-0.0042-0.08280.1012-0.04920.0332-0.1275-0.0202-0.1224-00.32080.0303-0.05910.23910.01970.2383-1.8926-27.1151-1.4659
150.2181-0.01240.02250.4156-0.0466-0.0252-0.1876-0.11470.2140.44240.1014-0.0977-0.0979-0.14720.00250.37010.0318-0.01770.2454-0.0040.1833-10.0622-15.24461.9107
160.254-0.0313-0.24260.2223-0.09580.17710.02110.07040.29030.08-0.1755-0.3626-0.25750.2133-0.00020.3621-0.0228-0.11890.2760.03230.30075.9303-20.85550.2586
170.0412-0.09030.03750.03530.03430.0674-0.09370.01710.19030.1645-0.0489-0.25930.09780.4123-0.0980.36120.0356-0.10060.29330.03160.2319.4922-36.20225.3779
180.33080.0493-0.12541.34830.23710.32670.01530.0312-0.03320.20210.01490.03070.0626-0.0106-00.2393-0.0001-0.03130.22340.02850.22632.1961-52.676-9.7422
190.23490.0992-0.08230.32370.1703-0.11730.0018-0.04090.0158-0.13860.1124-0.238-0.09340.06120.00150.25520.0037-0.04770.24460.00550.269.8328-44.7113-20.1814
200.3287-0.01890.09070.10130.13180.112-0.1484-0.05730.10210.69760.0748-0.4829-0.21610.129900.2737-0.0307-0.0460.27140.01890.263912.7999-31.2833-14.4203
210.75690.3228-0.10550.24380.31050.8631-0.00860.0051-0.0579-0.1269-0.003-0.2436-0.01310.2739-0.00030.1799-0.0098-0.02520.3158-0.00810.364818.0915-47.829-23.1304
220.16120.06250.02920.00760.03250.0075-0.0794-0.2156-0.20990.7529-0.04260.295-0.19360.1198-0.00020.4687-0.0420.04310.30320.02660.3322-18.2778-69.2194-16.8869
230.19730.2471-0.46410.66530.20860.79120.0050.0108-0.0880.12950.0292-0.04970.13720.0301-00.2137-0.0188-0.04690.1710.0290.2201-4.2036-66.5214-28.5544
240.1397-0.08660.00360.0559-0.00080.06960.02070.04020.07310.15730.06610.07370.1304-0.023900.3018-0.04450.02050.264-0.02330.34381.7979-44.4798-39.6619
250.2483-0.143-0.15440.1511-0.05130.3696-0.0796-0.0535-0.1408-0.16920.1369-0.4876-0.00370.20080.00010.1957-0.00660.00030.2779-0.02320.2869.1108-52.8495-38.396
260.13650.1049-0.00880.0791-0.0760.3428-0.12570.28970.0143-0.42790.12380.00790.19890.0606-00.2953-0.02790.03440.257-0.02540.31010.649-64.2088-47.7786
270.0103-0.0081-0.00620.10160.14240.2080.14560.0004-0.92220.01730.038-0.24020.55230.26410.01570.3284-0.0412-0.06240.19850.0350.3582-7.4995-76.6673-39.8332
280.2881-0.0166-0.22840.06150.18120.10910.0769-0.28120.0991-0.0703-0.04320.28440.0654-0.00640.00030.3207-0.09480.04350.33440.04190.3133-30.9229-66.4853-20.9486
290.6355-0.15210.21360.16650.08250.5184-0.0181-0.0904-0.10790.17510.07160.2080.0481-0.0322-00.2826-0.04980.02340.21890.0420.2341-25.2282-71.0505-28.4755
300.54540.0859-0.27050.2948-0.0420.31910.07680.0222-0.12340.1534-0.01790.05920.0357-0.003-00.2459-0.0645-0.00160.23070.01290.2573-28.4677-67.6802-39.8681
310.0926-0.0114-0.13070.08240.00250.05610.02520.0543-0.194-0.1046-0.0657-0.09560.08660.0256-0.00010.2434-0.019-0.04660.2546-0.00260.2663-18.4561-63.5609-51.67
320.49970.0830.28180.47250.45990.42060.03480.1899-0.1152-0.10390.05180.24380.1735-0.18480.00180.2247-0.0656-0.01490.24560.00220.3266-37.0586-68.4879-48.8425
330.6626-0.1285-0.11260.39090.39770.3471-0.0645-0.06160.09910.22330.08810.3208-0.00740.1833-0.02110.2864-0.05550.11870.3110.07540.3879-40.8342-60.4848-16.3816
340.7838-0.18120.05940.412-0.41170.6721-0.0007-0.0404-0.23370.1549-0.13110.39730.0736-0.1525-0.33230.249-0.10260.11640.27490.02890.4064-51.5649-58.6489-24.1768
350.25160.17370.12710.2492-0.10630.45870.1153-0.04160.0335-0.0254-0.09270.23170.0263-0.09170.00010.2212-0.0194-0.01170.276-0.01740.3661-47.3492-53.0885-44.3508
360.4841-0.3606-0.20030.76160.89781.08740.33180.2427-0.1839-0.7322-0.54041.0248-0.4826-0.6042-0.2395-0.1568-0.22990.16570.29860.02010.5657-61.6874-50.4797-30.6332
370.0696-0.0981-0.08150.070.03950.01420.01510.44560.2327-0.39720.09020.0896-0.0476-0.2229-0.00040.467-0.0580.02220.30340.0170.3246-4.59590.513-53.0831
380.2965-0.12220.12720.06110.02020.22360.0566-0.0015-0.0991-0.0967-0.06720.1288-0.1755-0.14960.00370.3412-0.06160.07450.27480.00480.22761.2832-11.67-55.248
390.3174-0.14660.16990.27750.11050.2162-0.00320.09420.0114-0.10590.0989-0.1107-0.11710.05540.00680.2844-0.07160.08410.24490.00380.23149.6152-12.6487-51.6433
400.3966-0.14020.25790.2580.00890.0991-0.10130.1112-0.02440.07020.1158-0.1768-0.07230.007100.2639-0.06190.0630.23790.02480.272814.949-9.1216-42.6989
410.1756-0.09380.03390.0555-0.05650.03410.09750.0552-0.02350.12940.02130.2338-0.0722-0.03150.00020.3317-0.04620.01620.2864-0.03960.33114.7442-34.8049-41.1798
420.2319-0.18020.19520.2168-0.08540.0041-0.03010.1173-0.2572-0.16750.0727-0.58790.13420.10860.05350.2218-0.03730.06620.2906-0.01710.300313.3826-32.2284-47.7337
430.2611-0.3048-0.02330.23090.05330.291-0.0365-0.0258-0.18910.36750.0043-0.3806-0.02920.2116-0.00030.2434-0.06570.00510.2836-0.00290.371819.965-20.1891-37.577
440.05990.0188-0.0060.01710.00160.01190.0193-0.19330.3717-0.39060.0716-0.5255-0.40450.5129-0.00030.3301-0.09690.07020.2441-0.02860.387618.3261-4.2267-42.1847
450.0250.00510.03450.05080.10290.06980.123-0.17870.1387-0.1873-0.14850.2947-0.6568-0.23880.00010.4301-0.05660.08890.2986-0.0140.2973-6.682-8.8863-63.4074
460.9485-0.02030.34781.174-0.13220.38250.08190.032-0.0169-0.08670.0174-0.043-0.12410.03080.17550.2899-0.02190.0830.2082-0.0010.1649-4.4381-25.9528-67.7312
470.0346-0.0621-0.13660.06290.1250.01860.1129-0.1836-0.0285-0.01520.00760.0044-0.0540.03360.00010.2555-0.0484-0.00570.308-0.00830.2944-13.0219-45.7726-54.1771
480.2325-0.2082-0.20370.47320.20890.0024-0.05890.2135-0.1769-0.32690.0818-0.0750.1126-0.1392-00.2829-0.01980.01070.2474-0.0170.2185-10.11-46.4701-64.928
490.16590.01430.04370.1283-0.08830.09190.0417-0.0078-0.4415-0.1285-0.0247-0.03150.30420.1694-0.00080.2983-0.01450.0570.2621-0.02530.34873.2711-46.6586-63.2157
500.21360.0310.29410.33910.1070.410.00350.0922-0.0075-0.009-0.0424-0.3136-0.02050.1646-0.00220.2957-0.02760.12720.2567-0.02190.283910.5674-32.0745-64.66
510.14560.0775-0.026-0.0228-0.0214-0.01210.0593-0.13710.3289-0.17310.12130.122-0.4752-0.17220.00010.3643-0.00380.05480.31610.01690.2927-19.1193-13.4347-69.1874
520.97140.2137-0.27750.84930.09040.43640.02110.02320.0418-0.1272-0.03220.1009-0.1315-0.009500.29030.0091-0.03440.25930.02760.1874-29.3399-27.7428-71.3335
530.44230.24490.2190.2893-0.02220.313-0.02430.0511-0.0576-0.136-0.02360.16840.0656-0.0504-00.22670.0049-0.04480.243-0.00450.3144-41.1179-42.6519-60.1951
540.29750.02480.33670.56090.14850.18850.03590.0783-0.1801-0.1654-0.03820.02240.01490.0763-00.30270.0078-0.01560.2876-0.00530.2282-26.2662-44.851-73.5096
550.0594-0.0386-0.10490.04-0.0190.06580.1530.02720.78690.0061-0.2529-0.2038-0.4060.34540.00020.4111-0.04670.00620.37960.03220.3609-32.262-9.0636-66.077
560.65230.1141-0.24520.83710.24460.53110.0330.01670.0376-0.1353-0.10260.0944-0.06590.0493-00.21080.0367-0.05910.25880.01210.2606-48.0105-16.0009-59.2662
570.02470.0133-0.10680.1152-0.32820.37740.0583-0.00110.0242-0.0332-0.05990.220.1253-0.130300.21870.0056-0.0370.3046-0.01280.3705-56.8956-24.7565-41.0957
580.55570.0358-0.21990.2470.12590.2685-0.04420.1168-0.2116-0.0719-0.09840.29170.2695-0.179-0.00220.24760.006-0.05850.319-0.01740.3351-56.4203-31.3272-60.2711
590.03610.05090.04280.04770.10780.10090.00980.12290.0261-0.22890.1022-0.1976-0.23270.43620.00030.2795-0.0358-0.07410.44270.05220.3215-37.1632-0.7206-55.4639
600.39980.1652-0.2255-0.0006-0.02920.2105-0.01150.0573-0.0749-0.1131-0.1039-0.0910.01260.1208-0.00010.19870.0035-0.06960.270.05260.322-38.87152.1407-42.6152
610.25430.00370.0666-0.0268-0.0296-0.024-0.01350.16690.0030.1144-0.0871-0.0575-0.19540.053-0.00030.22450.0248-0.06520.26750.04260.2895-46.54352.411-44.5988
620.1272-0.07790.1659-0.0593-0.3970.7102-0.0248-0.01540.03340.0269-0.0707-0.0143-0.03060.012900.18040.003-0.05090.24590.00860.2929-48.8965-2.5664-35.6518
630.2295-0.008-0.08950.1443-0.04410.0904-0.1833-0.13240.14060.1659-0.05960.0543-0.2302-0.106200.25760.011-0.01390.27590.0080.3142-47.5004-3.3823-19.7161
640.02980.0220.02980.030.01920.02580.0646-0.6056-0.21750.33530.13930.21670.1097-0.60080.00010.24270.01150.00740.4283-0.02010.3754-60.3996-5.707-24.1762
650.23880.0028-0.10060.13870.18680.3490.0098-0.16030.08380.0383-0.08720.39760.1032-0.2448-0.06010.17160.0003-0.02450.3098-0.02460.3851-59.8816-11.0284-34.0357
660.08790.0326-0.08870.0384-0.00540.042-0.0045-0.04850.1848-0.17110.13620.415-0.5373-0.43710.00140.22550.034-0.10230.2920.010.343-60.4285-2.8259-45.5494
670.15130.0780.06880.04450.0590.01340.06810.2961-0.2875-0.5184-0.324-0.0528-0.36720.3005-0.00250.2930.0341-0.09210.36250.04040.3147-29.20547.2717-46.9352
681.1021-0.03240.25270.195-0.03370.8963-0.03820.00750.0776-0.11360.00750.1083-0.06710.0138-0.00240.3033-0.0267-0.09130.1870.03620.2353-25.55359.7889-29.7826
690.1851-0.04180.36630.2450.00130.2295-0.1087-0.1177-0.01470.07310.0713-0.0527-0.030.001900.28630.0018-0.02910.22750.01450.2046-16.9916-0.3609-12.1183
700.22250.1631-0.1417-0.00730.05130.3211-0.0933-0.36550.0160.16790.07130.2058-0.2062-0.26960.00020.33110.0341-0.04370.31870.01530.3062-33.09036.6112-11.5578
710.0609-0.0362-0.00360.01790.02480.0458-0.28250.0560.6401-0.04140.04960.3064-0.28690.03660.00020.3772-0.006-0.11190.25680.01540.3662-39.206915.1056-24.6617
720.1245-0.07580.10370.0308-0.06850.00740.06580.3866-0.241-0.4576-0.03350.19990.35140.2912-00.414-0.0206-0.10770.2570.00570.2664-14.60857.8421-45.7397
730.3023-0.58440.25320.4912-0.01830.85290.05910.05070.0951-0.1530.0145-0.0161-0.06460.0262-0.00010.3028-0.04850.00010.20040.02330.2012-0.96063.3212-36.4458
740.1941-0.03210.25210.29830.01610.3319-0.1511-0.083-0.144-0.05440.141-0.2113-0.1197-0.03210.00250.2725-0.0269-0.04380.23670.03560.2241-3.51448.6618-24.465
750.0536-0.00580.10480.0225-0.02910.1291-0.0815-0.02930.0889-0.04660.05820.0960.0369-0.1536-0.00010.3068-0.03980.02420.2420.01670.30562.5424-18.186-23.0471
760.5653-0.13770.00990.11950.09460.1511-0.03110.00470.131-0.22950.0502-0.2929-0.05490.0363-0.00010.2501-0.03070.00030.2565-0.00730.24510.3992-10.3671-24.0248
770.19560.09-0.08520.0689-0.03560.0266-0.1124-0.2753-0.07410.24570.1938-0.0957-0.08170.01560.00010.2991-0.0123-0.04860.2715-0.00770.25972.28231.5316-15.0077
780.08570.1141-0.03870.1115-0.00610.0530.0303-0.22670.3969-0.161-0.00160.177-0.54370.00580.00020.4138-0.0066-0.01960.2302-0.02380.2945-4.437214.5553-23.1672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 158 )
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 192 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 27 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 94 )
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 132 )
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 158 )
10X-RAY DIFFRACTION10chain 'B' and (resid 159 through 183 )
11X-RAY DIFFRACTION11chain 'B' and (resid 184 through 192 )
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 27 )
13X-RAY DIFFRACTION13chain 'C' and (resid 28 through 106 )
14X-RAY DIFFRACTION14chain 'C' and (resid 107 through 132 )
15X-RAY DIFFRACTION15chain 'C' and (resid 133 through 158 )
16X-RAY DIFFRACTION16chain 'C' and (resid 159 through 183 )
17X-RAY DIFFRACTION17chain 'C' and (resid 184 through 192 )
18X-RAY DIFFRACTION18chain 'D' and (resid 3 through 106 )
19X-RAY DIFFRACTION19chain 'D' and (resid 107 through 132 )
20X-RAY DIFFRACTION20chain 'D' and (resid 133 through 158 )
21X-RAY DIFFRACTION21chain 'D' and (resid 159 through 192 )
22X-RAY DIFFRACTION22chain 'E' and (resid 4 through 27 )
23X-RAY DIFFRACTION23chain 'E' and (resid 28 through 122 )
24X-RAY DIFFRACTION24chain 'E' and (resid 123 through 132 )
25X-RAY DIFFRACTION25chain 'E' and (resid 133 through 158 )
26X-RAY DIFFRACTION26chain 'E' and (resid 159 through 183 )
27X-RAY DIFFRACTION27chain 'E' and (resid 184 through 192 )
28X-RAY DIFFRACTION28chain 'F' and (resid 4 through 37 )
29X-RAY DIFFRACTION29chain 'F' and (resid 38 through 70 )
30X-RAY DIFFRACTION30chain 'F' and (resid 71 through 132 )
31X-RAY DIFFRACTION31chain 'F' and (resid 133 through 158 )
32X-RAY DIFFRACTION32chain 'F' and (resid 159 through 192 )
33X-RAY DIFFRACTION33chain 'G' and (resid 4 through 54 )
34X-RAY DIFFRACTION34chain 'G' and (resid 55 through 122 )
35X-RAY DIFFRACTION35chain 'G' and (resid 123 through 158 )
36X-RAY DIFFRACTION36chain 'G' and (resid 159 through 192 )
37X-RAY DIFFRACTION37chain 'H' and (resid 4 through 27 )
38X-RAY DIFFRACTION38chain 'H' and (resid 28 through 54 )
39X-RAY DIFFRACTION39chain 'H' and (resid 55 through 106 )
40X-RAY DIFFRACTION40chain 'H' and (resid 107 through 122 )
41X-RAY DIFFRACTION41chain 'H' and (resid 123 through 132 )
42X-RAY DIFFRACTION42chain 'H' and (resid 133 through 158 )
43X-RAY DIFFRACTION43chain 'H' and (resid 159 through 183 )
44X-RAY DIFFRACTION44chain 'H' and (resid 184 through 192 )
45X-RAY DIFFRACTION45chain 'I' and (resid 4 through 27 )
46X-RAY DIFFRACTION46chain 'I' and (resid 28 through 122 )
47X-RAY DIFFRACTION47chain 'I' and (resid 123 through 132 )
48X-RAY DIFFRACTION48chain 'I' and (resid 133 through 158 )
49X-RAY DIFFRACTION49chain 'I' and (resid 159 through 172 )
50X-RAY DIFFRACTION50chain 'I' and (resid 173 through 192 )
51X-RAY DIFFRACTION51chain 'J' and (resid 4 through 27 )
52X-RAY DIFFRACTION52chain 'J' and (resid 28 through 122 )
53X-RAY DIFFRACTION53chain 'J' and (resid 123 through 158 )
54X-RAY DIFFRACTION54chain 'J' and (resid 159 through 192 )
55X-RAY DIFFRACTION55chain 'K' and (resid 4 through 27 )
56X-RAY DIFFRACTION56chain 'K' and (resid 28 through 122 )
57X-RAY DIFFRACTION57chain 'K' and (resid 123 through 158 )
58X-RAY DIFFRACTION58chain 'K' and (resid 159 through 192 )
59X-RAY DIFFRACTION59chain 'L' and (resid 4 through 27 )
60X-RAY DIFFRACTION60chain 'L' and (resid 28 through 54 )
61X-RAY DIFFRACTION61chain 'L' and (resid 55 through 70 )
62X-RAY DIFFRACTION62chain 'L' and (resid 71 through 132 )
63X-RAY DIFFRACTION63chain 'L' and (resid 133 through 158 )
64X-RAY DIFFRACTION64chain 'L' and (resid 159 through 169 )
65X-RAY DIFFRACTION65chain 'L' and (resid 170 through 183 )
66X-RAY DIFFRACTION66chain 'L' and (resid 184 through 192 )
67X-RAY DIFFRACTION67chain 'M' and (resid 4 through 27 )
68X-RAY DIFFRACTION68chain 'M' and (resid 28 through 122 )
69X-RAY DIFFRACTION69chain 'M' and (resid 123 through 158 )
70X-RAY DIFFRACTION70chain 'M' and (resid 159 through 183 )
71X-RAY DIFFRACTION71chain 'M' and (resid 184 through 192 )
72X-RAY DIFFRACTION72chain 'N' and (resid 4 through 27 )
73X-RAY DIFFRACTION73chain 'N' and (resid 28 through 106 )
74X-RAY DIFFRACTION74chain 'N' and (resid 107 through 122 )
75X-RAY DIFFRACTION75chain 'N' and (resid 123 through 132 )
76X-RAY DIFFRACTION76chain 'N' and (resid 133 through 158 )
77X-RAY DIFFRACTION77chain 'N' and (resid 159 through 183 )
78X-RAY DIFFRACTION78chain 'N' and (resid 184 through 192 )

+
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