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- PDB-4dyu: The crystal structure of DNA starvation/stationary phase protecti... -

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Basic information

Entry
Database: PDB / ID: 4dyu
TitleThe crystal structure of DNA starvation/stationary phase protection protein Dps from Yersinia pestis KIM 10
ComponentsDNA protection during starvation protein
KeywordsOXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / chromosome condensation / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm
Similarity search - Function
DNA protection during starvation protein, gammaproteobacteria / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...DNA protection during starvation protein, gammaproteobacteria / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA protection during starvation protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of DNA starvation/stationary phase protection protein Dps from Yersinia pestis KIM 10
Authors: Tan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
G: DNA protection during starvation protein
H: DNA protection during starvation protein
I: DNA protection during starvation protein
J: DNA protection during starvation protein
K: DNA protection during starvation protein
L: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,04737
Polymers230,01412
Non-polymers2,03425
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48880 Å2
ΔGint-823 kcal/mol
Surface area56740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.414, 105.102, 191.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsexperimentally unknown. It is predicted that the chains A,B,C,D,E,F,G,H,I,J,K and L may form a dodecamer.

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Components

#1: Protein
DNA protection during starvation protein


Mass: 19167.801 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM10+ / Gene: dps, y1677, Yersinia pestis, YPO2510, YP_2325 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic
References: UniProt: Q7CJ65, Oxidoreductases; Oxidizing metal ions
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Lithium Sulfate, 0.1M MES:NaOH, 35% (v/v) MPD, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012 / Details: mirror
RadiationMonochromator: Si crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.75→46.2 Å / Num. all: 56019 / Num. obs: 56019 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 11.2
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2776 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AK9
Resolution: 2.75→46.192 Å / SU ML: 0.89 / σ(F): 1.34 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 2829 5.06 %Random
Rwork0.1795 ---
all0.184 55867 --
obs0.184 55867 99.52 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.505 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6198 Å20 Å2-0 Å2
2--1.1183 Å20 Å2
3----2.7381 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14872 0 77 210 15159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815177
X-RAY DIFFRACTIONf_angle_d1.13620577
X-RAY DIFFRACTIONf_dihedral_angle_d16.9885504
X-RAY DIFFRACTIONf_chiral_restr0.0752388
X-RAY DIFFRACTIONf_plane_restr0.0042649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.7501-2.79750.37271540.2412558255897
2.7975-2.84840.34121330.219126232623100
2.8484-2.90320.37731360.233126272627100
2.9032-2.96240.33871470.221226152615100
2.9624-3.02680.36961320.233126452645100
3.0268-3.09720.35851460.216326552655100
3.0972-3.17470.31131560.209726002600100
3.1747-3.26050.2731390.182526192619100
3.2605-3.35640.31761380.175526342634100
3.3564-3.46470.29271260.159826672667100
3.4647-3.58850.25561490.165826232623100
3.5885-3.73210.25991460.150126562656100
3.7321-3.90190.21211300.151226662666100
3.9019-4.10750.23871470.159326312631100
4.1075-4.36460.21571250.13472686268699
4.3646-4.70130.23811380.12726522652100
4.7013-5.17390.22891640.164726672667100
5.1739-5.92120.28011400.225527132713100
5.9212-7.45510.28411360.210827312731100
7.4551-46.19880.21011470.19242770277097
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)
10.6945-0.44430.43140.8118-0.48480.7410.0906-0.28210.0040.23270.04880.2212-0.1353-0.31840.0070.12070.02790.12860.2583-0.11440.19418.368311.690950.2873
20.2039-0.1202-0.020.7311-0.61650.6552-0.0559-0.0014-0.16810.0686-0.03920.26640.041-0.1197-0.07280.19610.15550.02550.07770.02980.135711.01611.384142.542
30.9306-0.0723-0.20740.84730.10590.38410.1343-0.12340.1610.171-0.12530.1855-0.1909-0.2222-0.10710.14040.1290.04320.1492-0.11420.058810.92122.242845.2826
40.4504-0.18910.20340.6499-0.14710.7016-0.1698-0.0362-0.19460.2060.0636-0.07540.19560.1597-0.21510.11060.2258-0.0226-0.0201-0.06370.140350.4247-21.328116.3845
51.2912-0.59910.87370.8263-0.48031.0132-0.2612-0.12040.07270.13130.1857-0.2314-0.3073-0.08930.00830.19180.0527-0.00420.0315-0.03080.103138.6335-13.52049.838
60.78580.14280.80050.04760.25521.33180.05650.4549-0.0022-0.0330.0453-0.17480.11320.5943-0.02660.16860.14390.0480.46380.08430.299551.2488-17.54233.8417
70.3816-0.0821-0.181.13050.23481.42970.04420.0717-0.20110.0425-0.0085-0.16550.38810.12310.0160.24070.061-0.030.0568-0.1420.172637.8045-24.82628.4413
80.9932-0.64490.46031.0169-0.69871.1221-0.00450.0885-0.0865-0.1167-0.09260.1814-0.0728-0.1818-0.05990.12360.2196-0.03850.4637-0.14910.2463-6.108313.163329.4313
96.7136-4.4263-3.25023.94650.42037.4904-0.3511-0.0899-0.05260.36770.0218-0.31651.14050.58430.0070.26610.01520.0080.23790.01020.13545.6814-7.741450.3304
101.1371-1.28010.91211.9872-1.13320.79680.02750.17080.21840.1529-0.2956-0.319-0.11880.11780.1760.0409-0.0208-0.09640.3999-0.07310.12853.68664.189733.3948
110.542-0.12420.36932.1815-0.67860.43290.0559-0.30230.1050.50570.06130.0893-0.2436-0.2396-0.19980.17260.1040.04490.4273-0.09630.2478-6.81383.490440.5412
121.66320.26140.16911.1445-0.43991.1476-0.0230.0343-0.0228-0.09380.02890.29370.049-0.3698-0.1793-0.0654-0.0277-0.11410.2515-0.1220.2277-4.7999-1.849428.0772
137.50660.40420.89815.2948-1.00196.20970.20331.2092-0.1749-1.11370.1279-0.5130.12980.3157-0.15530.53830.05210.10190.3169-0.02550.263539.27263.4264-14.8777
140.8102-0.05640.23920.7738-0.00691.15640.06090.3009-0.0639-0.04820.012-0.32990.09980.4010.01970.01690.04270.02160.1022-0.00260.077252.533-0.22659.5699
155.4287-1.74970.9056.44552.27746.9068-0.0793-0.20630.39291.0295-0.11620.1740.35890.1206-0.14090.35380.0322-0.10460.2081-0.09730.327150.83299.308256.1194
160.628-0.0210.28711.4203-0.30781.5031-0.0062-0.0447-0.14630.10540.11810.07070.2567-0.0413-0.08730.05340.0599-0.03210.17720.05390.040634.7818-6.776856.0039
170.48920.04960.39510.25260.03890.61250.0972-0.0459-0.2840.0730.15340.01130.3209-0.05910.00320.0533-0.1126-0.163-0.0076-0.03650.089730.1933-11.461251.548
180.7690.2905-0.3280.4027-0.1660.7822-0.0187-0.1872-0.0910.2025-0.03910.10320.0579-0.21950.04190.24480.08570.20490.1288-0.049-0.136823.1128-3.866256.5374
199.08940.7157-0.40135.8003-0.35514.7756-0.0372-0.28110.0547-0.7057-0.138-0.4111-0.48020.1895-0.00510.45920.024-0.06140.1609-0.03660.225232.23437.18628.0131
200.3340.07060.06960.6880.17980.2682-0.02860.11330.1945-0.129-0.05680.0652-0.2476-0.1979-0.1160.07120.1057-0.10610.04880.17470.040923.20214.4698-0.5802
210.80850.05950.06181.1936-0.15210.2256-0.12630.17680.1511-0.30950.1920.2175-0.2491-0.27780.06990.25840.0308-0.00840.22220.07040.108220.81189.5488-11.0606
220.97050.19410.30731.79290.50911.2942-0.09070.12290.1412-0.30550.022-0.2823-0.15350.0207-0.00150.21110.03170.01520.1210.0750.125234.192711.3079-2.9781
231.97880.76850.00061.1823-0.2531.27770.0443-0.0626-0.37430.32080.0017-0.22910.3410.0187-0.01310.31170.11260.00460.11670.00790.111933.1109-27.412343.8078
241.83321.5065-0.35991.7017-0.18010.41480.326-0.1280.12370.33630.02160.00220.0720.00280.07440.1778-0.0065-0.0381-0.00810.04940.113637.9972-14.65340.9709
252.83680.9782-1.02131.3815-0.87710.75760.4474-0.5657-0.08530.7969-0.33-0.2004-0.25430.1365-0.11750.4282-0.0555-0.07320.15910.02310.189246.0899-17.429152.9665
260.8106-0.08670.30010.38860.0070.30510.0736-0.0107-0.11880.0199-0.0273-0.19750.19590.1083-0.06310.1740.3412-0.1528-0.03210.0220.09646.1789-21.414636.4469
270.76110.07390.20971.1665-0.2190.4730.05130.12230.0215-0.29110.05060.2968-0.0956-0.32040.02830.23270.0455-0.09460.4351-0.01010.08483.35156.8637-1.5369
281.56781.24651.24413.62732.34762.11970.01210.2107-0.0843-0.06940.1013-0.1937-0.220.0889-0.00340.12840.0309-0.02590.14870.04450.110411.981914.11649.8654
290.89620.05370.45020.48120.48590.8605-0.07610.05190.0713-0.20890.01380.1751-0.373-0.17140.04560.0560.1649-0.04890.27780.01770.13823.39118.03497.0247
300.38490.1010.31660.61130.020.6821-0.1122-0.1850.24760.1863-0.1120.2955-0.291-0.3124-0.22380.09930.1663-0.0208-0.1165-0.0981-0.138534.31227.744143.7823
310.2882-0.33330.09731.13240.46050.80390.05210.08370.1212-0.0908-0.0225-0.2784-0.33030.1314-0.05130.09590.02630.02070.0223-0.02890.042943.854720.332636.6539
321.3164-0.1020.21620.7123-0.19460.7425-0.0529-0.2234-0.07820.14430.0944-0.1372-0.1378-0.0695-0.06090.1517-0.0455-0.08380.00090.01170.071343.707914.840446.8458
336.71462.9576-0.45245.9363-0.44982.65150.2392-0.3686-0.22320.0845-0.09530.62910.2093-0.4318-0.12240.2025-0.2004-0.010.4657-0.12530.366-13.1949-13.101332.3403
341.41210.538-0.26550.6411-0.12870.63630.0267-0.00260.1420.0612-0.04980.13780.0641-0.1615-0.06480.2102-0.39170.08070.34440.04270.09720.1309-19.342814.7633
355.6716-0.297-5.85131.1431.25737.5126-0.1788-0.42890.1285-0.1790.2566-0.11140.31830.3734-0.06480.16680.0085-0.06510.1927-0.01810.138510.9994-14.844512.5655
360.40190.2262-0.24390.30450.06540.6893-0.0710.1906-0.1634-0.0504-0.03170.1930.1015-0.22080.03650.0994-0.1459-0.09190.23930.02110.24551.6676-20.84727.8877
371.88350.6819-0.13791.53420.06911.66130.0145-0.10630.0734-0.02580.1286-0.0383-0.05140.0833-0.05210.21-0.0459-0.11180.124-0.05820.22014.0756-8.30936.6795
380.5725-0.2144-0.14291.42940.27220.9590.0059-0.01540.3159-0.0638-0.0384-0.2743-0.18040.2292-0.13310.1254-0.056-0.06480.06210.02240.072150.224123.564221.0636
391.52260.12220.05840.4326-0.1870.783-0.1897-0.11350.0141-0.032-0.1292-0.0387-0.14460.1391-0.24230.1572-0.00980.1366-0.0009-0.0203-0.08237.758422.399524.6897
400.63650.2067-0.14620.4161-0.17150.8653-0.05350.05760.2992-0.1338-0.02890.0727-0.1934-0.1569-0.06840.277-0.1276-0.0213-0.01040.17480.015137.63830.875719.2471
417.53841.77151.94955.41372.68496.0375-0.7017-0.10260.2275-0.30480.22290.02810.4407-0.64410.0530.4807-0.10880.06680.264-0.10080.258331.4806-34.272.3144
420.79960.1251-0.26570.71640.52091.32290.2054-0.0948-0.0049-0.11010.0382-0.07150.1289-0.33930.10160.2424-0.1158-0.04990.0126-0.01070.10215.572-26.741921.0311
430.29780.3167-0.06520.99180.1621.0213-0.033-0.0673-0.08620.1388-0.28530.16430.3676-0.24-0.09080.31-0.1493-0.01650.00770.07690.160315.1151-31.298128.4666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 13:58)
2X-RAY DIFFRACTION2chain 'A' and (resseq 59:94)
3X-RAY DIFFRACTION3chain 'A' and (resseq 95:167)
4X-RAY DIFFRACTION4chain 'B' and (resseq 14:53)
5X-RAY DIFFRACTION5chain 'B' and (resseq 54:86)
6X-RAY DIFFRACTION6chain 'B' and (resseq 87:113)
7X-RAY DIFFRACTION7chain 'B' and (resseq 114:167)
8X-RAY DIFFRACTION8chain 'C' and (resseq 14:52)
9X-RAY DIFFRACTION9chain 'C' and (resseq 53:58)
10X-RAY DIFFRACTION10chain 'C' and (resseq 59:86)
11X-RAY DIFFRACTION11chain 'C' and (resseq 87:136)
12X-RAY DIFFRACTION12chain 'C' and (resseq 137:167)
13X-RAY DIFFRACTION13chain 'D' and (resseq 12:22)
14X-RAY DIFFRACTION14chain 'D' and (resseq 23:167)
15X-RAY DIFFRACTION15chain 'E' and (resseq 13:22)
16X-RAY DIFFRACTION16chain 'E' and (resseq 23:53)
17X-RAY DIFFRACTION17chain 'E' and (resseq 54:113)
18X-RAY DIFFRACTION18chain 'E' and (resseq 114:167)
19X-RAY DIFFRACTION19chain 'F' and (resseq 14:22)
20X-RAY DIFFRACTION20chain 'F' and (resseq 23:94)
21X-RAY DIFFRACTION21chain 'F' and (resseq 95:133)
22X-RAY DIFFRACTION22chain 'F' and (resseq 134:167)
23X-RAY DIFFRACTION23chain 'G' and (resseq 13:52)
24X-RAY DIFFRACTION24chain 'G' and (resseq 53:94)
25X-RAY DIFFRACTION25chain 'G' and (resseq 95:113)
26X-RAY DIFFRACTION26chain 'G' and (resseq 114:167)
27X-RAY DIFFRACTION27chain 'H' and (resseq 11:53)
28X-RAY DIFFRACTION28chain 'H' and (resseq 54:87)
29X-RAY DIFFRACTION29chain 'H' and (resseq 88:167)
30X-RAY DIFFRACTION30chain 'I' and (resseq 13:52)
31X-RAY DIFFRACTION31chain 'I' and (resseq 53:113)
32X-RAY DIFFRACTION32chain 'I' and (resseq 114:167)
33X-RAY DIFFRACTION33chain 'J' and (resseq 13:22)
34X-RAY DIFFRACTION34chain 'J' and (resseq 23:53)
35X-RAY DIFFRACTION35chain 'J' and (resseq 54:86)
36X-RAY DIFFRACTION36chain 'J' and (resseq 87:141)
37X-RAY DIFFRACTION37chain 'J' and (resseq 142:167)
38X-RAY DIFFRACTION38chain 'K' and (resseq 13:53)
39X-RAY DIFFRACTION39chain 'K' and (resseq 54:94)
40X-RAY DIFFRACTION40chain 'K' and (resseq 95:167)
41X-RAY DIFFRACTION41chain 'L' and (resseq 13:22)
42X-RAY DIFFRACTION42chain 'L' and (resseq 23:94)
43X-RAY DIFFRACTION43chain 'L' and (resseq 95:167)

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