[English] 日本語
Yorodumi
- PDB-7dm1: crystal structure of the M.tuberculosis phosphate ABC transport r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dm1
Titlecrystal structure of the M.tuberculosis phosphate ABC transport receptor PstS-1 in complex with Fab p4-36
Components
  • Phosphate-binding protein PstS 1
  • heavy chain
  • light chain
KeywordsTRANSPROT PROTEIN/IMMUNE SYSTEM / antibody / complex / TRANSPORT PROTEIN / TRANSPROT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


phosphate ion transport / phosphate ion transmembrane transport / cellular response to phosphate starvation / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / Modulation by Mtb of host immune system / cell adhesion / cell surface / extracellular region ...phosphate ion transport / phosphate ion transmembrane transport / cellular response to phosphate starvation / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / Modulation by Mtb of host immune system / cell adhesion / cell surface / extracellular region / plasma membrane / cytosol
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / : / PBP domain / PBP superfamily domain / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PHOSPHATE ION / Phosphate-binding protein PstS 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMa, B. / Freund, N. / Xiang, Y.
CitationJournal: Nat Commun / Year: 2021
Title: Human antibodies targeting a Mycobacterium transporter protein mediate protection against tuberculosis.
Authors: Watson, A. / Li, H. / Ma, B. / Weiss, R. / Bendayan, D. / Abramovitz, L. / Ben-Shalom, N. / Mor, M. / Pinko, E. / Bar Oz, M. / Wang, Z. / Du, F. / Lu, Y. / Rybniker, J. / Dahan, R. / Huang, ...Authors: Watson, A. / Li, H. / Ma, B. / Weiss, R. / Bendayan, D. / Abramovitz, L. / Ben-Shalom, N. / Mor, M. / Pinko, E. / Bar Oz, M. / Wang, Z. / Du, F. / Lu, Y. / Rybniker, J. / Dahan, R. / Huang, H. / Barkan, D. / Xiang, Y. / Javid, B. / Freund, N.T.
History
DepositionDec 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Phosphate-binding protein PstS 1
A: Phosphate-binding protein PstS 1
C: light chain
D: heavy chain
E: light chain
F: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9698
Polymers170,7796
Non-polymers1902
Water18,9881054
1
B: Phosphate-binding protein PstS 1
E: light chain
F: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4854
Polymers85,3903
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphate-binding protein PstS 1
C: light chain
D: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4854
Polymers85,3903
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.605, 78.144, 132.613
Angle α, β, γ (deg.)90.000, 90.360, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphate-binding protein PstS 1 / PstS-1 / 38-kDa glycolipoprotein / 38-kDa lipoprotein / P38 / Antigen Ag78 / Protein antigen B / Pab


Mass: 37023.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: pstS1, phoS1, Rv0934, MTCY08D9.05c / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P9WGU1
#2: Antibody light chain


Mass: 23325.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody heavy chain


Mass: 25040.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium iodide, 22% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→92.6 Å / Num. obs: 110145 / % possible obs: 96 % / Redundancy: 3.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.041 / Rrim(I) all: 0.075 / Net I/σ(I): 10.8 / Num. measured all: 343045 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.07-2.22.30.26139706176270.9250.2050.3332.995.4
6.22-92.63.20.0411380043760.9950.0280.052198.9

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pc3
Resolution: 2.1→92.6 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 5401 5.07 %
Rwork0.1864 101082 -
obs0.1886 106483 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.47 Å2 / Biso mean: 39.1833 Å2 / Biso min: 3.77 Å2
Refinement stepCycle: final / Resolution: 2.1→92.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11379 0 0 1054 12433
Biso mean---45.54 -
Num. residues----1534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.120.28561930.23643249344294
2.12-2.150.26861640.23743393355798
2.15-2.180.32261590.23473522368199
2.18-2.20.29762200.2373430365099
2.2-2.230.29071620.24173098326090
2.25-2.260.2538340.238377380793
2.26-2.290.28922060.22173450365699
2.29-2.330.25412110.20973444365599
2.33-2.370.27922040.21083455365999
2.37-2.40.25991900.20043392358299
2.4-2.450.24532030.207634963699100
2.45-2.490.28651910.207734583649100
2.49-2.540.30822110.211834193630100
2.54-2.590.26931840.203334923676100
2.59-2.650.27481890.198534863675100
2.65-2.710.27131690.20493485365499
2.71-2.780.27971690.196834933662100
2.78-2.850.22931720.194734923664100
2.85-2.930.22551570.19333510366799
2.93-3.030.24861710.2053502367399
3.03-3.140.24681730.20293491366499
3.14-3.260.22792110.18443459367099
3.26-3.410.20011860.18234933679100
3.41-3.590.21131930.17783490368399
3.59-3.820.22011890.16693438362799
3.82-4.110.17511680.15243534370299
4.11-4.520.17151930.1383493368699
4.52-5.180.16841860.14423508369499
5.18-6.520.20521800.18483551373199
6.52-92.60.26431630.21183586374998
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)
11.6894-0.19220.52371.5154-0.83520.64430.01980.2878-0.2488-0.32640.1638-0.07050.51350.3442-0.20880.24-0.0808-0.02140.3434-0.04840.26646.2415.068-11.389
22.10430.68190.311.28520.14713.3047-0.12290.1101-0.0795-0.12940.1478-0.1034-0.0519-0.217-0.07720.1142-0.044-0.01490.1760.01770.234349.13211.22-2.838
32.36671.05690.48951.36420.00083.88520.28640.0768-0.81040.0581-0.0359-0.47840.98860.2086-0.14190.3188-0.0113-0.0840.22890.00790.4544.18125.8193.062
40.613-0.24750.57130.52360.6162.81760.1298-0.0641-0.04720.09010.0456-0.0439-0.1064-0.2069-0.17950.1717-0.075-0.00180.22180.03220.242540.3659.60121.257
50.7211-0.70170.68951.18030.35663.55980.0328-0.1401-0.08220.28840.05060.08850.0713-0.2061-0.10590.2656-0.11630.04240.26270.05580.290943.4298.87332.582
61.94790.80211.16991.24260.71573.01160.3029-0.1567-0.27390.145-0.0497-0.0490.4304-0.1112-0.27240.2407-0.091-0.05780.22180.04520.328238.86621.13922.648
72.1115-0.2734-0.16421.67590.03272.5557-0.0394-0.4119-0.19920.1332-0.00260.48290.3479-0.5103-0.06550.3366-0.13310.04310.33290.04380.466650.47419.73723.87
80.20910.14330.86222.35530.73123.6603-0.0426-0.0848-0.0014-0.09370.04320.2718-0.1889-0.6812-0.04250.1332-0.0221-0.01840.28920.05590.288749.3565.00719.142
92.0476-1.227-0.06392.24370.30582.25840.0954-0.04680.03780.3508-0.0242-0.1704-0.0940.0449-0.10590.1914-0.0515-0.02140.2130.03110.225534.6475.26222.309
100.31870.51320.87472.49672.59313.31710.18010.2047-0.30010.20650.1551-0.3260.37480.289-0.40690.1708-0.0173-0.07270.2476-0.00920.371828.52215.7077.916
111.88421.61412.21761.59192.2174.11760.19940.1568-0.31010.20360.0657-0.09520.36750.0792-0.22610.1872-0.0255-0.01260.215-0.00350.320136.52517.5276.694
121.4613-0.05390.46180.3971-0.08582.5757-0.0060.2894-0.1816-0.00750.1162-0.2136-0.05630.3953-0.10930.1652-0.07190.00730.295-0.01920.309737.31812.514-5.134
131.51511.12060.55171.69961.02513.1763-0.05490.26050.0053-0.2728-0.0942-0.09080.20710.16240.09330.3340.04550.00610.32380.0460.16340.12-13.79237.544
140.8054-0.0473-0.9130.7791-0.79855.86820.10780.11230.05770.0276-0.07220.0745-0.279-0.088-0.02070.2163-0.02850.00410.27550.01260.20491.802-18.82254.825
153.4399-0.2161-0.3681.93320.03234.2598-0.152-0.0908-0.2501-0.05120.0201-0.01610.2442-0.09080.15570.2448-0.04970.0170.2153-0.00290.14261.793-12.17376.853
161.404-0.3946-0.34861.8859-0.59554.0781-0.01940.13160.09810.0435-0.0758-0.1334-0.11710.03160.06150.2123-0.07550.04280.27180.01030.2028-0.064-17.81665.866
170.9056-0.31031.52991.4558-0.87993.86180.22350.0715-0.102-0.012-0.04890.32410.2411-0.8435-0.19880.2756-0.10610.02860.4728-0.02520.269614.355-11.34162.251
181.0838-0.2997-0.23321.1925-0.82823.88450.05240.0747-0.0085-0.0577-0.00870.0890.0147-0.6494-0.04470.2944-0.0221-0.02770.4349-0.00130.22759.802-18.66444.182
192.4689-1.3958-0.03513.02463.5025.40590.08020.15110.02490.163-0.0114-0.25470.2479-0.054-0.14010.2643-0.00320.01490.26130.01340.29748.1623.20661.842
200.81870.19390.03392.68690.62143.5668-0.07760.08340.1666-0.15390.13030.0491-0.0890.011-0.10920.2282-0.03530.00390.22670.02610.276140.20721.26153.227
210.3174-0.006-0.22626.71914.4155.92930.12120.17020.1589-0.0938-0.0869-0.0283-0.1265-0.4902-0.05470.2336-0.0244-0.00330.333-0.00930.334240.10523.74661.565
220.4055-0.0843-0.2627-0.00210.4211.8336-0.0357-0.07230.02730.03330.0264-0.00570.0771-0.01670.01720.2512-0.00240.01620.22610.02340.274836.63618.40783.572
235.73751.02453.9045.7341.09712.68730.3091-0.1756-0.56050.55890.3647-0.28620.51481.0535-0.65630.31220.01340.02790.4893-0.00370.3642.24713.5100.67
241.44820.26450.00231.8895-0.51975.90.046-0.18820.07270.26090.0579-0.0672-0.20030.2258-0.08610.22540.02920.00890.2928-0.02380.269236.7219.61195.25
250.9006-0.90441.92651.6911-2.79665.4858-0.2079-0.44220.3410.51690.39090.1156-0.4287-0.4257-0.36460.1983-0.01690.04670.27930.01170.351724.8921.44466.106
261.34060.37090.01322.74870.08592.5101-0.11190.18860.1128-0.12210.08670.3325-0.0018-0.15080.01150.2316-0.0228-0.00240.25530.03050.304427.6345.11354.682
278.0249-0.95651.08083.0159-0.64312.324-0.51840.2591-0.0176-0.05110.38580.13920.06590.00460.14780.3067-0.06330.01690.2447-0.01380.27727.389-2.18555.359
281.20440.5039-0.80541.1846-0.40731.7532-0.11320.22170.0905-0.14150.20510.13050.00630.0057-0.1050.2193-0.0360.0050.2447-0.00390.327329.4124.79156.614
290.69210.5104-0.2660.795-1.51624.0984-0.10640.00350.0205-0.17390.02010.1180.32280.1107-0.00820.3227-0.03110.04910.2364-0.02730.26229.4736.84665.113
302.9125-0.794-0.81766.86170.80594.4777-0.16-0.12130.33450.94410.05020.10870.11320.10550.13260.2784-0.01450.01870.2923-0.02040.286423.37815.78692.156
312.5904-0.4983-0.94031.87331.04222.02640.11770.1440.2065-0.0451-0.1423-0.0133-0.1303-0.172-0.00210.23230.00980.01620.2556-0.00220.242525.10615.96484.6
325.5253-4.7367-2.42688.2622.93773.90260.03450.0527-0.3094-0.1186-0.17660.4463-0.0707-0.16960.24950.2442-0.0076-0.00750.2848-0.02140.315515.60313.91587.413
330.54930.1357-0.35412.4192-0.7422.52160.0395-0.0144-0.00870.40850.18940.3840.3237-0.6667-0.18390.6098-0.19640.08350.55230.03740.4901-3.653-22.287100.52
341.50520.3076-0.18812.23530.1433.84320.1467-0.1235-0.08420.1560.10370.07860.8001-0.3258-0.23370.6571-0.17690.02360.43060.00030.35944.667-25.463100.96
350.8117-0.3490.11110.6141-1.02762.62670.0227-0.19130.0374-0.0570.0370.06710.32540.0179-0.03590.5089-0.20.08390.4678-0.02760.35419.382-21.344127.427
361.3082-0.01580.13071.3382-0.65185.09880.1014-0.13470.0588-0.06960.04680.04920.0036-0.1085-0.110.4126-0.12590.03550.5607-0.06130.35667.011-21.011139.218
375.97761.62543.68343.29090.91718.80380.0519-0.24880.0747-0.0744-0.05880.33080.8013-0.7399-0.02240.3583-0.14970.03040.637-0.0150.36315.26-28.826142.043
380.1275-0.0688-0.75530.09180.66395.92830.2269-0.25410.3765-0.16390.3221-0.4087-0.38220.6058-0.70310.468-0.18060.07370.4694-0.09180.534419.049-5.175110.588
395.5284-2.6061-0.36215.69280.92894.40440.2459-0.2061-0.2741-0.02510.3106-0.53930.11470.9917-0.6160.3686-0.07620.09180.4872-0.03980.39524.036-10.12699.677
401.38340.5174-0.53032.56380.02744.49480.07470.0237-0.01720.01970.0735-0.0982-0.52060.0605-0.18610.5238-0.10320.0970.3956-0.01340.407412.119-7.25999.452
412.7092-1.6758-1.27221.56440.18333.56420.17430.21210.44740.13720.0894-0.0452-0.51240.2322-0.26370.5889-0.13640.14390.3433-0.05090.460516.369-0.988100.066
422.4482-0.0016-0.57942.16980.02614.7821-0.08180.00280.3113-0.15910.3503-0.101-0.64770.3895-0.25920.5322-0.12510.08420.4498-0.06080.40214.025-3.248108.144
432.9360.50621.17841.7975-0.95918.7650.19290.26720.05410.15920.0482-0.28980.69190.1309-0.28320.5208-0.10840.07340.3969-0.03140.358714.329-16.92893.043
441.4612-1.35681.67612.2858-0.75992.5918-0.1061-0.0488-0.0160.25570.0237-0.0056-0.28450.08130.10940.371-0.12490.11230.4845-0.07030.38218.849-12.205129.812
453.0158-1.53830.50912.9757-0.74950.68880.07640.0683-0.1972-0.0337-0.12020.17590.0466-0.00850.0060.4274-0.07330.04380.4773-0.05970.290119.79-19.37129.502
463.6052-3.86251.8526.1869-1.4131.0528-0.145-0.18320.274-0.09460.1864-0.40870.1785-0.1125-0.01420.4501-0.11990.06810.5314-0.06440.317728.78-16.156131.208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:35 )A18 - 35
2X-RAY DIFFRACTION2( CHAIN A AND RESID 36:74 )A36 - 74
3X-RAY DIFFRACTION3( CHAIN A AND RESID 75:96 )A75 - 96
4X-RAY DIFFRACTION4( CHAIN A AND RESID 97:132 )A97 - 132
5X-RAY DIFFRACTION5( CHAIN A AND RESID 133:166 )A133 - 166
6X-RAY DIFFRACTION6( CHAIN A AND RESID 167:189 )A167 - 189
7X-RAY DIFFRACTION7( CHAIN A AND RESID 190:206 )A190 - 206
8X-RAY DIFFRACTION8( CHAIN A AND RESID 207:235 )A207 - 235
9X-RAY DIFFRACTION9( CHAIN A AND RESID 236:254 )A236 - 254
10X-RAY DIFFRACTION10( CHAIN A AND RESID 255:275 )A255 - 275
11X-RAY DIFFRACTION11( CHAIN A AND RESID 276:302 )A276 - 302
12X-RAY DIFFRACTION12( CHAIN A AND RESID 303:351 )A303 - 351
13X-RAY DIFFRACTION13( CHAIN B AND RESID 18:52 )B18 - 52
14X-RAY DIFFRACTION14( CHAIN B AND RESID 53:132 )B53 - 132
15X-RAY DIFFRACTION15( CHAIN B AND RESID 133:166 )B133 - 166
16X-RAY DIFFRACTION16( CHAIN B AND RESID 167:235 )B167 - 235
17X-RAY DIFFRACTION17( CHAIN B AND RESID 236:268 )B236 - 268
18X-RAY DIFFRACTION18( CHAIN B AND RESID 269:351 )B269 - 351
19X-RAY DIFFRACTION19( CHAIN C AND RESID 5:26 )C5 - 26
20X-RAY DIFFRACTION20( CHAIN C AND RESID 27:80 )C27 - 80
21X-RAY DIFFRACTION21( CHAIN C AND RESID 81:96 )C81 - 96
22X-RAY DIFFRACTION22( CHAIN C AND RESID 97:158 )C97 - 158
23X-RAY DIFFRACTION23( CHAIN C AND RESID 159:169 )C159 - 169
24X-RAY DIFFRACTION24( CHAIN C AND RESID 170:216 )C170 - 216
25X-RAY DIFFRACTION25( CHAIN D AND RESID 1:17 )D1 - 17
26X-RAY DIFFRACTION26( CHAIN D AND RESID 18:62 )D18 - 62
27X-RAY DIFFRACTION27( CHAIN D AND RESID 63:78 )D63 - 78
28X-RAY DIFFRACTION28( CHAIN D AND RESID 79:110 )D79 - 110
29X-RAY DIFFRACTION29( CHAIN D AND RESID 111:134 )D111 - 134
30X-RAY DIFFRACTION30( CHAIN D AND RESID 135:160 )D135 - 160
31X-RAY DIFFRACTION31( CHAIN D AND RESID 161:203 )D161 - 203
32X-RAY DIFFRACTION32( CHAIN D AND RESID 204:228 )D204 - 228
33X-RAY DIFFRACTION33( CHAIN E AND RESID 5:37 )E5 - 37
34X-RAY DIFFRACTION34( CHAIN E AND RESID 38:101 )E38 - 101
35X-RAY DIFFRACTION35( CHAIN E AND RESID 102:137 )E102 - 137
36X-RAY DIFFRACTION36( CHAIN E AND RESID 138:204 )E138 - 204
37X-RAY DIFFRACTION37( CHAIN E AND RESID 205:216 )E205 - 216
38X-RAY DIFFRACTION38( CHAIN F AND RESID 1:17 )F1 - 17
39X-RAY DIFFRACTION39( CHAIN F AND RESID 18:33 )F18 - 33
40X-RAY DIFFRACTION40( CHAIN F AND RESID 34:62 )F34 - 62
41X-RAY DIFFRACTION41( CHAIN F AND RESID 63:78 )F63 - 78
42X-RAY DIFFRACTION42( CHAIN F AND RESID 79:99 )F79 - 99
43X-RAY DIFFRACTION43( CHAIN F AND RESID 100:119 )F100 - 119
44X-RAY DIFFRACTION44( CHAIN F AND RESID 120:160 )F120 - 160
45X-RAY DIFFRACTION45( CHAIN F AND RESID 161:205 )F161 - 205
46X-RAY DIFFRACTION46( CHAIN F AND RESID 206:228 )F206 - 228

+
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