[English] 日本語
Yorodumi
- PDB-6qtl: Caffeine recognizing nanobody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qtl
TitleCaffeine recognizing nanobody
Components(VHH) x 2
KeywordsBIOSYNTHETIC PROTEIN / design nanoboy
Function / homologyCAFFEINE
Function and homology information
Biological speciesCamelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLesne, J. / Guichou, J.F. / Labesse, G. / Cohen-Gonsaud, M.
CitationJournal: To Be Published
Title: Structural basis for chemically-induced homodimerization of a single domain antibody
Authors: Lesne, J.x.
History
DepositionFeb 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: VHH
A: VHH
B: VHH
C: VHH
D: VHH
E: VHH
F: VHH
G: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,30512
Polymers104,5298
Non-polymers7774
Water10,827601
1
H: VHH
B: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3263
Polymers26,1322
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-13 kcal/mol
Surface area10530 Å2
MethodPISA
2
A: VHH
C: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3263
Polymers26,1322
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-13 kcal/mol
Surface area10510 Å2
MethodPISA
3
D: VHH
G: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3263
Polymers26,1322
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-12 kcal/mol
Surface area10430 Å2
MethodPISA
4
E: VHH
F: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3263
Polymers26,1322
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-13 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.260, 60.990, 87.670
Angle α, β, γ (deg.)90.000, 93.690, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody
VHH


Mass: 13022.530 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#2: Antibody
VHH


Mass: 13109.608 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE / Caffeine (data page)


Mass: 194.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10N4O2 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M MgCl2, NaAc pH 5.5 100mM, PEG 2k 25%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→58.4 Å / Num. obs: 54239 / % possible obs: 91 % / Redundancy: 9.055 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rrim(I) all: 0.15 / Χ2: 0.934 / Net I/σ(I): 10.47 / Num. measured all: 491122 / Scaling rejects: 1756
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.29.1410.7553.0111232014757122880.9310.79983.3
2.2-2.59.1890.5044.4412383414171134770.9680.53395.1
2.5-39.1170.2288.3210992212817120570.9930.24294.1
3-48.9320.08717.98793241023788810.9980.09286.8
4-58.8670.05327.1732268367436390.9990.05799
5-68.830.05426.2214402165016310.9990.05898.8
6-108.5650.04628.9615126178517660.9990.04898.9
10-58.47.8520.03236.9392652250010.03595.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QSK
Resolution: 2.25→58.4 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1650 4.14 %
Rwork0.1935 38235 -
obs0.1963 39885 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.58 Å2 / Biso mean: 27.714 Å2 / Biso min: 0.06 Å2
Refinement stepCycle: final / Resolution: 2.25→58.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 56 605 7953
Biso mean--18.75 27.04 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077504
X-RAY DIFFRACTIONf_angle_d0.92910164
X-RAY DIFFRACTIONf_chiral_restr0.0541084
X-RAY DIFFRACTIONf_plane_restr0.0051344
X-RAY DIFFRACTIONf_dihedral_angle_d11.2014324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.31620.38031090.23632483259275
2.3162-2.3910.32821260.23992785291184
2.391-2.47640.29041340.24343107324194
2.4764-2.57560.34081430.22593296343999
2.5756-2.69280.31251380.23013303344199
2.6928-2.83480.27871520.22423308346099
2.8348-3.01240.2541420.21443328347099
3.0124-3.2450.28751410.20423269341098
3.245-3.57150.24941370.17873163330094
3.5715-4.08820.21111430.168633663509100
4.0882-5.15020.19891470.141833733520100
5.1502-58.41950.22741380.17253454359299
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)
12.8506-0.4473-0.88550.6156-0.35051.4816-0.22111.05050.0249-0.4173-0.02890.23430.12790.33680.22130.5531-0.0017-0.01330.47390.05240.251713.32184.575670.7051
23.59471.55230.83534.70842.71732.25420.17940.6197-0.1376-0.5946-0.209-0.35-0.44180.0338-0.0080.402-0.04240.0120.49620.14150.203319.54858.349777.7888
30.15180.29820.22472.20940.30631.364-0.0510.04680.0338-0.26050.05180.2937-0.327-0.1046-0.4560.1998-0.0507-0.040.36210.26080.18713.38157.56284.529
42.11631.4653.71343.1153.57996.9985-0.00190.12090.05380.0076-0.03360.3414-0.7048-0.72340.04940.46770.1329-0.03330.90780.21380.3134-2.00737.976676.265
50.3937-0.3822-0.32121.4072-0.10840.79170.08710.7743-0.3479-0.22170.18150.1470.23630.5872-0.25780.1840.0371-0.0880.42380.0340.287913.50790.263986.7536
63.10713.39031.91215.66943.92232.9723-0.06070.1531-0.41440.1943-0.8011-0.03341.1928-0.55080.850.52730.0963-0.06730.3293-0.11360.48996.1097-7.156181.4099
71.3438-0.33561.03651.2155-0.40191.8869-0.25960.3817-0.1353-0.1479-0.2091-0.28550.02690.82620.18830.14580.14790.06550.7471-0.01710.459221.72911.962781.4838
87.97222.4284.33322.7021.56382.89340.15140.8841-0.66590.1870.2607-0.14550.55230.9937-0.38610.39480.10270.00030.5792-0.11280.260210.337-2.578273.3494
90.78410.12291.53331.83541.01256.5871-0.15290.2424-0.0553-0.27020.0936-0.1668-0.40480.45560.06720.2071-0.0449-0.08860.45720.09720.172710.354810.007681.4424
101.79390.04510.06850.8251-0.59360.4333-0.06320.5751-0.2671-0.37250.0395-0.04030.2898-0.21020.02810.3411-0.19850.09930.13310.02790.114421.920533.441411.3332
113.96293.15472.61775.06253.43433.3110.0130.04050.01270.2507-0.1666-0.24790.0622-0.0259-0.11360.212-0.19570.01670.1718-0.06120.215128.243437.214618.1484
124.20611.19430.49351.32420.73431.6234-0.33-0.28070.2177-0.07290.0723-0.0392-0.31520.1178-0.03630.2252-0.1388-0.15850.04920.00050.186922.133737.146125.0755
135.24362.38383.96551.25362.21814.9551-0.12290.10730.55360.05610.18860.3940.01670.23820.28620.31630.1810.00380.87960.13930.51686.760238.477116.808
141.90680.1726-0.55471.34460.17870.4793-0.2908-0.5089-0.27290.13750.1078-0.04680.06950.22470.03280.2090.0360.03380.01960.08380.1720.958227.774224.9673
151.0234-0.572-0.02663.0944-0.44311.2994-0.0036-0.0906-0.03970.098-0.1354-0.663-0.13750.198-0.25360.30790.015-0.00090.06040.03930.347429.465131.668419.1691
165.19830.58711.46095.24241.33886.5346-0.11020.1573-0.1682-0.12540.33950.33980.0848-0.2794-0.1240.1083-0.0020.00480.1610.08620.146316.262532.211516.9727
171.94310.66970.23581.85390.46363.5837-0.1464-0.06610.2224-0.06850.1502-0.0918-0.2847-0.1324-0.13760.1878-0.061-0.05760.07620.03710.224519.006939.577121.4832
180.44750.46220.3830.50040.51891.251-0.3415-0.4126-0.1735-0.1132-0.11020.00290.1169-0.1007-0.46410.13610.01780.0660.46240.19960.1991-11.5532.889797.404
195.0051-1.90673.21341.8127-0.40452.6635-0.2769-0.4102-0.02430.5415-0.0854-0.08220.1348-0.1146-0.2420.30020.0125-0.03760.54410.15720.1443-3.61972.1163103.9624
203.2119-0.77361.30591.4957-0.71152.7507-0.0655-0.0303-0.6869-0.2211-0.0695-0.00580.15150.2947-0.25530.1552-0.02590.00890.17720.0470.2381-0.01591.278792.6209
210.7319-0.56750.27792.3144-0.4332.9662-0.1919-0.46450.1290.0722-0.0409-0.0838-0.364-0.010.19020.12-0.0164-0.00320.3910.04950.1767-1.034410.719596.9467
222.56541.02150.89630.39290.23432.0052-0.0819-0.0490.0457-0.1217-0.05840.02240.090.09690.17640.1787-0.0384-0.03730.1540.05750.156-6.72264.559891.2488
232.71940.07940.73040.29990.23880.34960.06950.1151-0.1999-0.2636-0.0573-0.14720.17090.21130.05140.12260.0123-0.03120.31410.15870.2241-0.3323-0.687894.6007
240.51980.73940.47361.55130.73330.8809-0.0641-0.3726-0.1194-0.0001-0.25450.31590.1988-0.00120.13560.2686-0.07840.0510.56650.1040.2174-2.809233.615338.2656
252.9559-0.1896-0.22542.6626-0.45883.6669-0.03880.0184-0.2870.21430.02670.04540.0995-0.0313-0.06210.1577-0.0010.0110.15060.04160.16328.658335.640636.684
263.18630.2448-0.91314.4822-1.58995.10460.0267-0.34880.3560.1955-0.24250.043-0.00190.23340.17830.27230.0538-0.0140.2075-0.03080.19844.827542.0538.411
274.4884-0.2228-0.3691.34960.26242.5004-0.2224-0.3016-0.67770.08890.17090.16920.421-0.36460.01020.3165-0.05940.080.22470.02950.22055.262132.32233.7258
282.8277-0.9502-1.28013.13960.13840.62580.1714-0.4825-0.03850.1068-0.2931-0.17830.09520.4483-0.07870.21460.1027-0.01740.7265-0.01010.196938.1727-0.168554.7367
293.2999-0.7828-1.56841.08550.64381.19620.4115-0.08320.6368-0.0105-0.149-0.2145-0.619-0.1543-0.22170.22380.09570.0030.3639-0.06660.152730.24743.934747.6893
301.62620.7305-0.13181.1529-0.7990.66880.0865-0.61750.1219-0.0409-0.04150.16260.28920.1545-0.07610.14830.10840.02010.39430.05250.169128.6199-5.623451.7884
314.7055-1.6134-0.58283.0546-0.01892.27080.2109-0.2944-0.1158-0.3029-0.00460.14470.27770.24240.37150.08510.08610.02880.3340.04520.122335.7294-1.109545.714
325.7432-0.8794-0.52632.7864-0.24332.59370.2774-0.64140.77060.11890.0138-0.1882-0.45140.1815-0.21790.2064-0.00740.00950.199-0.10290.303724.96889.089351.8313
332.8990.7057-0.45370.71070.04771.0607-0.14330.0555-0.5914-0.071-0.1564-0.24780.1490.124-0.07990.07240.0470.05820.67650.10440.381645.1614-1.534844.9876
341.55820.44330.23071.0605-0.97251.18730.2827-0.34270.0297-0.2855-0.30110.17180.0364-0.26610.04490.20330.0721-0.09120.2709-0.09160.302344.191930.458780.5532
356.3925-6.0696-5.18476.30294.73984.9816-0.3018-1.00760.15690.77330.18090.18880.24570.1712-0.22410.3315-0.01370.01090.3036-0.09860.273337.616631.040185.9566
365.8222-0.4843-1.66621.94320.74634.69360.4529-0.21170.41780.1303-0.0455-0.184-0.2657-0.524-0.24220.1455-0.0123-0.04460.17640.02880.197830.624133.210180.4349
371.2845-0.24280.17230.4479-0.3610.4703-0.046-0.00110.25-0.0310.26280.0481-0.1841-0.01140.03680.3008-0.0742-0.010.0723-0.0410.239734.756832.575570.6511
384.1031-0.32231.23971.53870.00680.90230.3064-0.3041-0.17-0.5831-0.14580.14090.4325-0.1007-0.02880.38680.0075-0.07410.1120.05310.262829.149822.820776.2083
390.85030.9672-0.12133.1551-1.27950.64910.2135-1.05860.14440.85930.1871-0.01620.3383-0.0953-0.14820.30640.0216-0.02320.53440.04680.204232.918225.108286.8797
403.22990.5563-0.64550.7322-0.12054.7458-0.0069-0.4141-0.7079-0.3530.20950.00750.4694-0.35120.02280.3447-0.0047-0.00470.19050.08310.290641.583323.698675.3397
412.47310.0702-0.34160.735-0.58181.38790.1705-0.1931-0.0501-0.10530.0024-0.031-0.0573-0.2387-0.00540.05950.04010.02150.2206-0.0830.374134.461635.498478.1307
421.9067-0.33860.19070.89620.12380.04650.0996-0.29390.2545-0.0306-0.0707-0.0099-0.127-0.2589-0.09560.12130.04790.02070.2894-0.12830.313428.039339.305880.0547
432.9762-1.6053-1.85646.5739-1.0315.10830.29210.1646-0.1629-0.3650.1699-0.23270.15820.27540.20410.14510.03980.0170.1943-0.21690.276748.697929.49973.5937
440.639-0.6076-1.15154.1958-3.32917.4837-0.22620.04280.0185-0.00890.17130.27490.4089-0.4520.13990.1886-0.0156-0.01690.3738-0.11090.153512.435228.053461.69
450.1698-0.10290.26860.32510.5422.5933-0.02740.0430.0925-0.1733-0.26470.25510.2781-0.6094-0.35290.16740.0921-0.00320.20120.13110.09417.535.154261.3851
461.1982-2.174-1.32364.53912.80955.4289-0.14350.0731-0.19610.211-0.067-0.07120.69140.49290.12220.19630.05080.04480.21910.00180.205327.891932.44163.9517
474.90472.1173-0.29544.513-2.18944.66640.1415-0.70060.16280.1407-0.214-0.1433-0.53030.04930.04150.23680.01630.04920.1836-0.04360.280422.845742.794569.2373
482.95311.99170.02983.10550.77621.69850.0617-0.18070.48190.0813-0.17530.1817-0.1796-0.45090.12190.1940.10690.05740.34010.11420.251913.568540.738563.6932
491.5185-0.4912-0.33722.055-0.17612.19050.31040.12560.254-0.1534-0.0809-0.0530.07770.1785-0.08970.19030.06340.02550.2020.06690.155224.649635.529959.7675
501.82260.1404-2.24270.7158-0.25566.61790.01990.03060.0564-0.1644-0.2064-0.0910.81950.25780.19110.25650.10440.00730.27660.07320.174121.063729.784663.5734
510.6710.4587-0.97991.4618-0.30771.55410.15260.27260.0967-0.1380.00430.1707-0.0845-0.6567-0.27860.15290.05650.00030.48270.14520.207812.5534.525929.5056
522.05030.5656-0.9421.38710.75192.2736-0.0854-0.1446-0.0542-0.2874-0.2698-0.11930.1307-0.5525-0.2420.1580.08210.05560.3090.07020.161615.10342.296340.2453
534.54870.44062.52964.0559-1.9823.29370.3283-0.0717-0.38510.43730.1558-0.04740.70490.6657-0.11470.39630.1771-0.00190.7136-0.00840.241629.5594-2.243731.0721
540.1135-0.1919-0.06780.32030.14090.08470.0053-0.1520.44320.14950.18660.0371-0.2013-0.1671-0.0182-0.01940.25720.0920.32480.09530.270118.333811.208239.8984
551.8357-0.3501-0.00090.60590.18810.73970.138-0.15430.1924-0.0097-0.1173-0.167-0.1776-0.5486-0.1138-0.03340.35690.12630.4070.16480.206816.433110.331131.0628
561.35870.13791.02312.88190.58982.08180.0278-0.04240.04140.1152-0.1740.20540.2188-0.015-0.32630.19920.02280.0090.13830.07070.184317.1876-0.222236.398
570.71070.1115-1.75050.9852-0.8496.7887-0.06860.17610.0819-0.08690.15820.08090.3587-0.11260.00880.14530.03120.00260.41350.10170.193217.2992-0.902336.5533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 4 through 19 )H4 - 19
2X-RAY DIFFRACTION2chain 'H' and (resid 20 through 29 )H20 - 29
3X-RAY DIFFRACTION3chain 'H' and (resid 30 through 41 )H30 - 41
4X-RAY DIFFRACTION4chain 'H' and (resid 42 through 47 )H42 - 47
5X-RAY DIFFRACTION5chain 'H' and (resid 48 through 62 )H48 - 62
6X-RAY DIFFRACTION6chain 'H' and (resid 63 through 69 )H63 - 69
7X-RAY DIFFRACTION7chain 'H' and (resid 70 through 79 )H70 - 79
8X-RAY DIFFRACTION8chain 'H' and (resid 80 through 93 )H80 - 93
9X-RAY DIFFRACTION9chain 'H' and (resid 94 through 119 )H94 - 119
10X-RAY DIFFRACTION10chain 'A' and (resid 4 through 19 )A4 - 19
11X-RAY DIFFRACTION11chain 'A' and (resid 20 through 29 )A20 - 29
12X-RAY DIFFRACTION12chain 'A' and (resid 30 through 41 )A30 - 41
13X-RAY DIFFRACTION13chain 'A' and (resid 42 through 47 )A42 - 47
14X-RAY DIFFRACTION14chain 'A' and (resid 48 through 75 )A48 - 75
15X-RAY DIFFRACTION15chain 'A' and (resid 76 through 85 )A76 - 85
16X-RAY DIFFRACTION16chain 'A' and (resid 86 through 102 )A86 - 102
17X-RAY DIFFRACTION17chain 'A' and (resid 103 through 120 )A103 - 120
18X-RAY DIFFRACTION18chain 'B' and (resid 4 through 19 )B4 - 19
19X-RAY DIFFRACTION19chain 'B' and (resid 20 through 29 )B20 - 29
20X-RAY DIFFRACTION20chain 'B' and (resid 30 through 47 )B30 - 47
21X-RAY DIFFRACTION21chain 'B' and (resid 48 through 85 )B48 - 85
22X-RAY DIFFRACTION22chain 'B' and (resid 86 through 102 )B86 - 102
23X-RAY DIFFRACTION23chain 'B' and (resid 103 through 120 )B103 - 120
24X-RAY DIFFRACTION24chain 'C' and (resid 4 through 18 )C4 - 18
25X-RAY DIFFRACTION25chain 'C' and (resid 19 through 62 )C19 - 62
26X-RAY DIFFRACTION26chain 'C' and (resid 63 through 86 )C63 - 86
27X-RAY DIFFRACTION27chain 'C' and (resid 87 through 120 )C87 - 120
28X-RAY DIFFRACTION28chain 'D' and (resid 4 through 29 )D4 - 29
29X-RAY DIFFRACTION29chain 'D' and (resid 30 through 47 )D30 - 47
30X-RAY DIFFRACTION30chain 'D' and (resid 48 through 85 )D48 - 85
31X-RAY DIFFRACTION31chain 'D' and (resid 86 through 102 )D86 - 102
32X-RAY DIFFRACTION32chain 'D' and (resid 103 through 114 )D103 - 114
33X-RAY DIFFRACTION33chain 'D' and (resid 115 through 120 )D115 - 120
34X-RAY DIFFRACTION34chain 'E' and (resid 4 through 18 )E4 - 18
35X-RAY DIFFRACTION35chain 'E' and (resid 19 through 29 )E19 - 29
36X-RAY DIFFRACTION36chain 'E' and (resid 30 through 41 )E30 - 41
37X-RAY DIFFRACTION37chain 'E' and (resid 42 through 54 )E42 - 54
38X-RAY DIFFRACTION38chain 'E' and (resid 55 through 69 )E55 - 69
39X-RAY DIFFRACTION39chain 'E' and (resid 70 through 79 )E70 - 79
40X-RAY DIFFRACTION40chain 'E' and (resid 80 through 93 )E80 - 93
41X-RAY DIFFRACTION41chain 'E' and (resid 94 through 102 )E94 - 102
42X-RAY DIFFRACTION42chain 'E' and (resid 103 through 114 )E103 - 114
43X-RAY DIFFRACTION43chain 'E' and (resid 115 through 120 )E115 - 120
44X-RAY DIFFRACTION44chain 'F' and (resid 4 through 9 )F4 - 9
45X-RAY DIFFRACTION45chain 'F' and (resid 10 through 41 )F10 - 41
46X-RAY DIFFRACTION46chain 'F' and (resid 42 through 54 )F42 - 54
47X-RAY DIFFRACTION47chain 'F' and (resid 55 through 69 )F55 - 69
48X-RAY DIFFRACTION48chain 'F' and (resid 70 through 85 )F70 - 85
49X-RAY DIFFRACTION49chain 'F' and (resid 86 through 102 )F86 - 102
50X-RAY DIFFRACTION50chain 'F' and (resid 103 through 121 )F103 - 121
51X-RAY DIFFRACTION51chain 'G' and (resid 4 through 29 )G4 - 29
52X-RAY DIFFRACTION52chain 'G' and (resid 30 through 41 )G30 - 41
53X-RAY DIFFRACTION53chain 'G' and (resid 42 through 47 )G42 - 47
54X-RAY DIFFRACTION54chain 'G' and (resid 48 through 75 )G48 - 75
55X-RAY DIFFRACTION55chain 'G' and (resid 76 through 93 )G76 - 93
56X-RAY DIFFRACTION56chain 'G' and (resid 94 through 102 )G94 - 102
57X-RAY DIFFRACTION57chain 'G' and (resid 103 through 120 )G103 - 120

+
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