[English] 日本語
Yorodumi
- PDB-4dyu: The crystal structure of DNA starvation/stationary phase protecti... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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


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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.31 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

-
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

-
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

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)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)

+
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