[English] 日本語
Yorodumi
- PDB-7p4y: GlnK2 from Methanothermococcus thermolithotrophicus in the apo st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p4y
TitleGlnK2 from Methanothermococcus thermolithotrophicus in the apo state at a resolution of 2.3 A
ComponentsGlnK2 from Methanothermococcus thermolithotrophicus
KeywordsSIGNALING PROTEIN / PII-family protein / protein inhibitor / regulation / methanococcales / methanogenic archaea / thermophile / ATP binding / 2-oxoglutarate / conformational changes / T-loop / nitrogen-metabolism
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMueller, M.-C. / Wagner, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Int J Mol Sci / Year: 2021
Title: The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales .
Authors: Muller, M.C. / Wagner, T.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GlnK2 from Methanothermococcus thermolithotrophicus
B: GlnK2 from Methanothermococcus thermolithotrophicus
C: GlnK2 from Methanothermococcus thermolithotrophicus
D: GlnK2 from Methanothermococcus thermolithotrophicus
E: GlnK2 from Methanothermococcus thermolithotrophicus
F: GlnK2 from Methanothermococcus thermolithotrophicus
G: GlnK2 from Methanothermococcus thermolithotrophicus
H: GlnK2 from Methanothermococcus thermolithotrophicus
I: GlnK2 from Methanothermococcus thermolithotrophicus
J: GlnK2 from Methanothermococcus thermolithotrophicus
K: GlnK2 from Methanothermococcus thermolithotrophicus
L: GlnK2 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,20925
Polymers176,74812
Non-polymers46113
Water1,874104
1
A: GlnK2 from Methanothermococcus thermolithotrophicus
B: GlnK2 from Methanothermococcus thermolithotrophicus
C: GlnK2 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2585
Polymers44,1873
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-38 kcal/mol
Surface area12720 Å2
MethodPISA
2
D: GlnK2 from Methanothermococcus thermolithotrophicus
E: GlnK2 from Methanothermococcus thermolithotrophicus
F: GlnK2 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3648
Polymers44,1873
Non-polymers1775
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-60 kcal/mol
Surface area12500 Å2
MethodPISA
3
G: GlnK2 from Methanothermococcus thermolithotrophicus
H: GlnK2 from Methanothermococcus thermolithotrophicus
I: GlnK2 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2936
Polymers44,1873
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-52 kcal/mol
Surface area12760 Å2
MethodPISA
4
J: GlnK2 from Methanothermococcus thermolithotrophicus
K: GlnK2 from Methanothermococcus thermolithotrophicus
L: GlnK2 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2936
Polymers44,1873
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-50 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.461, 103.460, 178.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein
GlnK2 from Methanothermococcus thermolithotrophicus


Mass: 14729.015 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Strain: DSM 2095 / Tissue: / / Cell: / / Cell line: / / Gene: glnk2 / Organ: / / Variant: / / Plasmid: pET-28a(+) / Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / Variant (production host): /
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.7 Å3/Da / Density % sol: 54.48 % / Description: Transparent square
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MtGlnK2 apo was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500 mM NaCl on a 96-Well MRC 2-Drop Crystallization Plates in ...Details: MtGlnK2 apo was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500 mM NaCl on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). Drop of 0.6 ul of protein was mixed with 0.6 ul of the crystallization solution. The reservoir contained 90 ul of the following crystallization solution 35 % w/v Pentaerythritol ethoxylate (15/4 EO/OH) and 100 mM HEPES pH 7.5.
PH range: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.42
ReflectionResolution: 2.3→73.16 Å / Num. obs: 70360 / % possible obs: 96.2 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.055 / Rrim(I) all: 0.144 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6 % / Rmerge(I) obs: 1.151 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3519 / CC1/2: 0.671 / Rpim(I) all: 0.508 / Rrim(I) all: 1.259 / % possible all: 81.3

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J9D
Resolution: 2.3→73.16 Å / Cross valid method: THROUGHOUT / σ(F): 85.43 / Phase error: 42.05 / Stereochemistry target values: TWIN_LSQ_F
Details: The refinement was performed with the following twin operator: k,h,-l
RfactorNum. reflection% reflection
Rfree0.2445 3625 5.31 %
Rwork0.2215 66701 -
obs0.233 70326 82.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.84 Å2 / Biso mean: 37.6095 Å2 / Biso min: 15.89 Å2
Refinement stepCycle: final / Resolution: 2.3→73.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9066 0 13 104 9183
Biso mean--43.38 32.51 -
Num. residues----1164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.340.3232740.29561287136131
2.34-2.380.3334850.30021426151134
2.38-2.430.26381020.28061673177540
2.43-2.480.31141360.28712073220949
2.48-2.530.24021090.27392484259359
2.53-2.590.27871380.26052872301068
2.59-2.660.26421520.25563073322572
2.66-2.730.38921620.25513253341577
2.73-2.810.3021810.24723648382985
2.81-2.90.28142290.2513884411392
2.9-30.26552470.24743997424494
3-3.120.24632230.24024054427795
3.12-3.260.2642010.24244066426795
3.26-3.440.24762290.23734050427995
3.44-3.650.24722130.22744068428195
3.65-3.930.25012240.22034079430395
3.93-4.330.23162110.21464119433095
4.33-4.950.24132510.19794105435694
4.95-6.240.24162370.21294138437595
6.24-73.160.23322210.23664352457395
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)
12.88380.3648-0.80151.6828-0.62423.4355-0.1085-0.3342-0.08920.5358-0.1176-0.286-0.29640.14760.13190.51630.0058-0.1120.28220.09320.1618-38.2619-36.469329.7637
22.0267-0.31540.12372.7506-1.21783.1081-0.0234-0.2014-0.09730.45170.0223-1.0940.12290.3630.11310.22750.0499-0.16520.3018-0.0730.302-34.4511-36.333823.4927
34.11370.8868-1.09964.02511.18353.93180.1523-0.2268-0.37320.2007-0.1274-0.34430.4040.0297-0.07250.2649-0.0073-0.10210.24570.09540.2686-53.067-47.783619.5049
43.21371.5688-0.2722.54060.20982.94820.12330.1449-0.59020.10250.1303-0.49770.3750.3107-0.19220.30730.0247-0.01450.1514-0.02080.2778-44.1439-47.983220.0601
54.5759-1.0249-0.99226.8340.22924.0533-0.0320.21170.34030.2214-0.00260.3463-0.1484-0.286-0.05040.17540.0568-0.03130.1606-0.05030.2479-48.9134-26.336912.3254
60.88311.0287-1.62373.0741-3.9225.27120.11590.6198-0.0882-0.099-0.08830.9692-0.037-0.6837-0.02890.28870.0813-0.17160.5222-0.28770.8366-54.3019-29.24986.7022
79.98582.91140.78345.06921.29275.34190.3206-1.10160.29171.3537-0.5634-0.17610.3614-0.04610.13810.61330.0339-0.03540.33380.13890.3433-45.6043-27.32226.6191
82.61990.52010.29425.4270.13122.3688-0.28380.45970.3901-0.62350.2301-0.258-0.23620.25460.01020.13460.02320.0170.27320.05250.2093-44.6072-24.996411.4552
92.42061.73090.79585.35530.42751.42940.08910.4427-0.2223-0.45660.0863-0.23850.35050.08970.00690.2204-0.05140.10580.367-0.16160.1279-44.456-38.118210.3931
106.67830.614-2.50594.34660.45271.6501-0.37711.0557-0.3359-0.51620.53250.01440.7486-0.1018-0.23920.52010.0044-0.19620.4068-0.10840.3998-55.9256-45.37124.5542
113.96420.29951.04943.69750.21242.53020.4061-0.45380.2010.7987-0.08210.80230.274-0.2813-0.12450.3170.01860.17260.348-0.0160.3897-16.189-15.509729.6777
124.73570.9725-0.1990.1986-0.04090.0085-0.0933-0.1708-0.57680.43020.22130.83560.57460.2233-0.11190.65830.03550.1420.42790.00310.6227-20.6988-21.919128.0552
133.1722-0.81610.29711.2992-1.69172.4247-0.2831-0.34070.06430.69140.1764-0.1416-0.07730.4781-0.36070.5824-0.03940.15310.4132-0.27180.1652-2.3459-12.921830.7134
142.161-0.2281-0.16563.37840.02552.22160.107-0.38740.22430.58070.20590.8574-0.4467-0.4111-0.27090.45860.06420.13860.28260.03460.4707-17.4251-11.325229.7759
153.4694-0.7578-0.37063.1458-0.88790.3546-0.0138-0.01630.33140.24670.00950.4199-0.0055-0.10730.0789-0.00450.0729-0.03930.30420.09330.6723-14.5084-7.839222.5517
162.6667-1.8925-0.47485.28131.27453.046-0.15030.05230.50950.1638-0.13230.47220.2723-0.10320.26590.2572-0.0832-0.06170.3659-0.07730.2922-18.114-26.152912.0558
172.5909-0.3425-0.91172.03550.23071.67050.0978-0.69080.45390.1020.203-0.1728-0.16120.1266-0.14380.3331-0.0685-0.02290.3717-0.06140.112.2633-3.267620.6508
183.2791-0.5912-0.18965.09430.04061.3555-0.0505-0.48750.12510.3310.2013-0.23780.04660.2359-0.09080.4835-0.12040.04730.357-0.02160.062.6938-10.599821.9275
194.3387-0.1227-1.00153.19490.31041.5370.09030.11930.4272-0.13240.1511-0.4992-0.1902-0.011-0.19550.2422-0.0670.00310.33990.07080.15692.02-3.871615.4867
203.1395-0.95-2.51473.14050.25535.70290.1493-0.42291.00080.4816-0.16451.015-0.6883-0.3383-0.19350.43170.07650.16790.384-0.13410.8591-17.2325-0.815326.1341
213.4935-1.55390.02588.1382-2.91022.37870.00530.20960.1164-0.3357-0.12790.37660.2071-0.08050.16880.1522-0.02410.00990.2444-0.14030.2511-2.8461-25.431612.269
220.3024-0.39870.17313.33132.33092.4324-0.14880.61490.25-0.2763-0.1002-0.5469-0.00370.45730.1560.39450.04180.07990.3731-0.00780.32442.4546-22.57146.5735
235.2640.7698-0.3272.7578-0.69693.3918-0.1337-0.6669-0.14630.8774-0.00630.37850.0581-0.48060.15260.46880.020.08940.4741-0.0611-0.1238-6.1409-24.31426.042
243.0339-0.48031.85645.4205-0.57381.5605-0.07870.20620.2257-0.0695-0.08910.17520.0748-0.0710.110.1321-0.02360.07680.3081-0.01830.2084-5.9389-24.40219.8014
251.282-0.08250.77717.18140.59250.5720.0002-0.0525-0.1699-0.16560.09570.80590.0511-0.1506-0.06840.14990.01950.01560.2812-0.08160.2659-10.0031-22.088513.4079
262.8199-0.54554.12081.7462-2.18837.2036-0.14961.5882-0.1361-0.4720.4404-0.2480.29980.6891-0.09280.35160.00290.05130.4626-0.04630.34798.3859-5.07437.4054
279.42253.1775.63925.48272.32684.1078-0.06941.4442-0.1362-0.5440.5092-0.35390.15480.766-0.24160.5066-0.1689-0.08660.4279-0.03750.24510.9895-7.68062.4234
282.77450.27970.83372.4586-1.3773.46550.1327-0.56820.50760.23840.32570.24360.0269-0.3712-0.25780.3248-0.017-0.05210.3287-0.08550.2244-68.846415.624832.2992
293.9939-3.33722.0818.4577-3.10815.5302-0.5195-0.20210.15590.45750.3968-0.99340.00390.353-0.27830.36670.0263-0.03350.4343-0.32940.1182-62.84951.524832.1894
302.5401-0.53121.38961.7895-2.17734.0414-0.1345-0.4180.47040.33130.096-0.7235-0.2051-0.1280.08330.327-0.007-0.02290.2398-0.11470.3424-62.787315.879631.3175
316.48354.296-1.76224.4406-2.37733.5713-0.34340.40030.9213-0.23920.36570.5467-0.11-0.6649-0.16410.3460.0665-0.07630.2809-0.00510.2928-77.671918.162814.6299
323.12641.75520.31533.5350.41871.3580.15670.13030.0140.83010.4646-0.04760.13530.2445-0.44980.31820.0026-0.17310.3273-0.05850.3008-53.8119-2.008422.5148
337.72691.71881.23336.26242.27995.38730.08940.2706-0.52040.755-0.13250.22430.24340.16330.03180.3650.0701-0.12180.3248-0.06620.1761-67.8426-4.887723.012
340.48470.361-0.67436.219-0.13191.4678-0.14-0.1016-0.0961-0.16220.1451-0.93940.17920.3118-0.10740.19940.0074-0.04340.3372-0.06490.2396-55.0107-1.673216.5389
353.7467-1.3738-1.35491.8537-0.40385.717-0.0665-0.53030.21220.29570.6658-0.5405-0.59621.1656-0.34450.3004-0.0191-0.19540.4348-0.18040.6894-52.941916.579829.229
367.1587-0.7205-1.38953.7440.52143.4383-0.23040.0724-0.1991-0.2811-0.03260.37190.09450.05360.34010.2840.0125-0.01610.13-0.09280.1953-70.47738.032113.1287
372.7842-0.3488-0.77091.81720.12251.07250.002-0.0128-0.42360.0408-0.25640.2208-0.2754-0.0411-0.22830.3342-0.06480.22660.5011-0.1528-0.3276-78.66680.558617.2917
384.86191.7765-2.49763.1707-3.02557.31020.05770.60950.6891-0.23110.40740.90780.0686-0.519-0.33920.27370.0006-0.05820.2643-0.01150.2429-75.75316.305711.2719
397.67173.2372-0.91874.7263-0.24862.9683-0.0904-0.35380.6711-0.0771-0.25810.6018-0.5405-0.66420.06190.2690.1368-0.04730.35730.00530.3005-79.85711.802417.6352
400.61010.0089-0.82224.3333-0.71011.85560.0966-0.0102-0.0859-0.8082-0.1295-0.3873-0.05850.0397-0.04220.3745-0.11790.09920.3113-0.02080.2187-57.5739-0.5975.5232
411.7275-0.077-0.111.7438-1.30196.79680.16940.6297-0.4559-0.1630.02680.07910.2065-0.1868-0.18260.37080.0186-0.06820.3575-0.17820.3026-15.9497-15.03457.0938
423.06031.1904-0.90346.4377-2.02675.6904-0.02530.4082-0.40520.26150.2137-0.2391-0.1966-0.6268-0.2040.26560.0022-0.00470.3679-0.12360.3165-15.1327-7.511257.5979
431.91010.6175-1.31552.088-2.04563.8841-0.11990.3284-0.8058-0.2256-0.0254-0.410.27530.26880.01240.37560.04470.02230.3545-0.16720.3093-11.7091-16.318356.6236
442.7537-0.0065-1.09632.21570.44193.49850.0887-0.0345-0.6970.2375-0.01180.27960.5931-0.04480.11770.2899-0.0297-0.02510.1636-0.05150.2656-20.976-17.011871.7227
453.12851.79130.69953.5591-0.54783.2112-0.2010.3690.0011-0.5475-0.0248-0.3003-0.0135-0.03630.25870.3158-0.0537-0.01220.2718-0.01410.1413-5.63152.908766.7654
463.6818-1.8444-0.69193.88370.52573.46260.0191-0.13530.3122-0.33270.2738-0.186-0.02230.193-0.16070.2322-0.03550.00520.25410.0340.1572-3.25351.590572.6461
474.0836-0.5345-0.09144.6569-0.35086.81210.0590.3666-0.3587-0.0146-0.0863-1.50410.65170.93730.14750.46120.1515-0.09250.3263-0.09590.4662-1.1861-16.608259.96
488.1074-0.91812.37812.67971.10444.6210.0243-0.44980.25260.1246-0.43120.2090.0902-0.38460.33280.1555-0.0230.08040.224-0.07270.2118-24.7387-3.170475.9501
493.8706-0.3373-2.88151.8995-1.00376.3748-0.1503-0.84370.89780.1677-0.0682-0.3695-0.51840.02720.19840.25920.0799-0.15190.4386-0.2560.6775-21.89791.665381.7497
506.4063-0.28751.05815.61380.7447.6460.28360.78850.3565-0.8042-0.3840.41640.4313-0.39490.23490.346-0.06580.10040.37550.01340.2323-24.8843-4.656661.2988
515.4586-0.82630.08853.2242-2.18781.8803-0.0121-0.5530.13690.3316-0.3232-0.044-0.0726-0.34390.2530.273-0.0632-0.00210.2129-0.10640.2057-24.0807-6.332477.9067
522.26850.3945-0.03091.7806-0.7190.8970.23870.0375-0.3451-0.265-0.50790.01490.3399-0.386-0.17470.3366-0.02910.00390.2985-0.25220.1349-21.9744-10.003773.9287
531.42270.9012-1.84436.0601-2.06042.5470.0778-0.1385-0.20131.0745-0.2138-0.69860.1361-0.06090.11760.3537-0.0251-0.09950.35170.00020.1804-5.82762.914485.2282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 55 )A-2 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 112 )A56 - 112
3X-RAY DIFFRACTION3chain 'B' and (resid -2 through 81 )B-2 - 81
4X-RAY DIFFRACTION4chain 'B' and (resid 82 through 112 )B82 - 112
5X-RAY DIFFRACTION5chain 'C' and (resid -1 through 22 )C-1 - 22
6X-RAY DIFFRACTION6chain 'C' and (resid 23 through 28 )C23 - 28
7X-RAY DIFFRACTION7chain 'C' and (resid 29 through 55 )C29 - 55
8X-RAY DIFFRACTION8chain 'C' and (resid 56 through 88 )C56 - 88
9X-RAY DIFFRACTION9chain 'C' and (resid 89 through 101 )C89 - 101
10X-RAY DIFFRACTION10chain 'C' and (resid 102 through 112 )C102 - 112
11X-RAY DIFFRACTION11chain 'D' and (resid -2 through 22 )D-2 - 22
12X-RAY DIFFRACTION12chain 'D' and (resid 23 through 28 )D23 - 28
13X-RAY DIFFRACTION13chain 'D' and (resid 29 through 55 )D29 - 55
14X-RAY DIFFRACTION14chain 'D' and (resid 56 through 88 )D56 - 88
15X-RAY DIFFRACTION15chain 'D' and (resid 89 through 95 )D89 - 95
16X-RAY DIFFRACTION16chain 'D' and (resid 96 through 112 )D96 - 112
17X-RAY DIFFRACTION17chain 'E' and (resid -1 through 22 )E-1 - 22
18X-RAY DIFFRACTION18chain 'E' and (resid 23 through 55 )E23 - 55
19X-RAY DIFFRACTION19chain 'E' and (resid 56 through 95 )E56 - 95
20X-RAY DIFFRACTION20chain 'E' and (resid 96 through 112 )E96 - 112
21X-RAY DIFFRACTION21chain 'F' and (resid -1 through 22 )F-1 - 22
22X-RAY DIFFRACTION22chain 'F' and (resid 23 through 28 )F23 - 28
23X-RAY DIFFRACTION23chain 'F' and (resid 29 through 55 )F29 - 55
24X-RAY DIFFRACTION24chain 'F' and (resid 56 through 81 )F56 - 81
25X-RAY DIFFRACTION25chain 'F' and (resid 82 through 100 )F82 - 100
26X-RAY DIFFRACTION26chain 'F' and (resid 101 through 105 )F101 - 105
27X-RAY DIFFRACTION27chain 'F' and (resid 106 through 112 )F106 - 112
28X-RAY DIFFRACTION28chain 'G' and (resid -1 through 28 )G-1 - 28
29X-RAY DIFFRACTION29chain 'G' and (resid 29 through 55 )G29 - 55
30X-RAY DIFFRACTION30chain 'G' and (resid 56 through 95 )G56 - 95
31X-RAY DIFFRACTION31chain 'G' and (resid 96 through 112 )G96 - 112
32X-RAY DIFFRACTION32chain 'H' and (resid -1 through 28 )H-1 - 28
33X-RAY DIFFRACTION33chain 'H' and (resid 29 through 56 )H29 - 56
34X-RAY DIFFRACTION34chain 'H' and (resid 57 through 95 )H57 - 95
35X-RAY DIFFRACTION35chain 'H' and (resid 96 through 112 )H96 - 112
36X-RAY DIFFRACTION36chain 'I' and (resid -1 through 9 )I-1 - 9
37X-RAY DIFFRACTION37chain 'I' and (resid 10 through 55 )I10 - 55
38X-RAY DIFFRACTION38chain 'I' and (resid 56 through 81 )I56 - 81
39X-RAY DIFFRACTION39chain 'I' and (resid 82 through 95 )I82 - 95
40X-RAY DIFFRACTION40chain 'I' and (resid 96 through 112 )I96 - 112
41X-RAY DIFFRACTION41chain 'J' and (resid -2 through 22 )J-2 - 22
42X-RAY DIFFRACTION42chain 'J' and (resid 23 through 55 )J23 - 55
43X-RAY DIFFRACTION43chain 'J' and (resid 56 through 88 )J56 - 88
44X-RAY DIFFRACTION44chain 'J' and (resid 89 through 112 )J89 - 112
45X-RAY DIFFRACTION45chain 'K' and (resid -1 through 56 )K-1 - 56
46X-RAY DIFFRACTION46chain 'K' and (resid 57 through 95 )K57 - 95
47X-RAY DIFFRACTION47chain 'K' and (resid 96 through 112 )K96 - 112
48X-RAY DIFFRACTION48chain 'L' and (resid -2 through 22 )L-2 - 22
49X-RAY DIFFRACTION49chain 'L' and (resid 23 through 28 )L23 - 28
50X-RAY DIFFRACTION50chain 'L' and (resid 29 through 55 )L29 - 55
51X-RAY DIFFRACTION51chain 'L' and (resid 56 through 81 )L56 - 81
52X-RAY DIFFRACTION52chain 'L' and (resid 82 through 100 )L82 - 100
53X-RAY DIFFRACTION53chain 'L' and (resid 101 through 112 )L101 - 112

+
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://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