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- PDB-6hvq: The structure of Dps from Listeria innocua soaked before soaking ... -

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Basic information

Entry
Database: PDB / ID: 6hvq
TitleThe structure of Dps from Listeria innocua soaked before soaking experiments with Zn, Co and La
Components(DNA protection during starvation protein) x 2
KeywordsMETAL BINDING PROTEIN / Dps / metal binding. cage shaped protein / ferroxidase / itron translocation
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Dps protein family signature 2. / 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 ...Dps protein family signature 2. / 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
LANTHANUM (III) ION / DNA protection during starvation protein
Similarity search - Component
Biological speciesListeria innocua serovar 6a
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsZeth, K. / Okuda, M.
CitationJournal: Inorg.Chem. / Year: 2019
Title: Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps.
Authors: Zeth, K. / Sancho-Vaello, E. / Okuda, M.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _exptl_crystal_grow.temp
Revision 1.2May 15, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_alt_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.ptnr1_symmetry / _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.ptnr2_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,37656
Polymers108,4306
Non-polymers6,94550
Water15,727873
1
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,751112
Polymers216,86112
Non-polymers13,890100
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area53590 Å2
ΔGint-843 kcal/mol
Surface area67330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.020, 88.020, 274.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
DNA protection during starvation protein / Ferritin-like protein / Non-heme iron-containing ferritin


Mass: 18070.553 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: dps, flp, fri, lin0942 / Production host: Escherichia coli (E. coli)
References: UniProt: P80725, Oxidoreductases; Oxidizing metal ions
#2: Protein DNA protection during starvation protein / Ferritin-like protein / Non-heme iron-containing ferritin


Mass: 18077.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: dps, flp, fri, lin0942 / Production host: Escherichia coli (E. coli)
References: UniProt: P80725, Oxidoreductases; Oxidizing metal ions
#3: Chemical...
ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: La
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 873 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growMethod: vapor diffusion, hanging drop / Details: 25% PEG 3350 pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 157727 / % possible obs: 97.1 % / Redundancy: 8 % / Net I/σ(I): 1.42
Reflection shellResolution: 1.9→1.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 1.9→43.456 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 20.09
RfactorNum. reflection% reflection
Rfree0.1938 7873 4.99 %
Rwork0.16 --
obs0.1617 157670 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 50 873 8309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047618
X-RAY DIFFRACTIONf_angle_d0.65610289
X-RAY DIFFRACTIONf_dihedral_angle_d13.0534571
X-RAY DIFFRACTIONf_chiral_restr0.041116
X-RAY DIFFRACTIONf_plane_restr0.0041331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.28361990.26933734X-RAY DIFFRACTION72
1.9216-1.94420.33172090.27883930X-RAY DIFFRACTION77
1.9442-1.96790.2722170.27234185X-RAY DIFFRACTION82
1.9679-1.99280.28762300.2564536X-RAY DIFFRACTION88
1.9928-2.01910.25622610.24044955X-RAY DIFFRACTION97
2.0191-2.04670.2852730.24165209X-RAY DIFFRACTION100
2.0467-2.0760.24842710.22635096X-RAY DIFFRACTION100
2.076-2.1070.27222690.20665169X-RAY DIFFRACTION100
2.107-2.13990.2782650.20265124X-RAY DIFFRACTION100
2.1399-2.1750.22522610.19435123X-RAY DIFFRACTION100
2.175-2.21250.19422750.19135160X-RAY DIFFRACTION100
2.2125-2.25270.26352730.22075131X-RAY DIFFRACTION100
2.2527-2.2960.24192670.1945125X-RAY DIFFRACTION100
2.296-2.34290.18482740.17165152X-RAY DIFFRACTION100
2.3429-2.39380.20922690.17195136X-RAY DIFFRACTION100
2.3938-2.44950.20982730.17455159X-RAY DIFFRACTION100
2.4495-2.51080.20562670.17145143X-RAY DIFFRACTION100
2.5108-2.57860.20752710.16965162X-RAY DIFFRACTION100
2.5786-2.65450.20972700.16745098X-RAY DIFFRACTION100
2.6545-2.74020.18052670.16265139X-RAY DIFFRACTION100
2.7402-2.83810.17552710.16245187X-RAY DIFFRACTION100
2.8381-2.95170.20952720.16675104X-RAY DIFFRACTION100
2.9517-3.0860.23132700.17095110X-RAY DIFFRACTION100
3.086-3.24860.22852750.17495170X-RAY DIFFRACTION100
3.2486-3.45210.20442660.1585132X-RAY DIFFRACTION100
3.4521-3.71850.2012740.15095116X-RAY DIFFRACTION100
3.7185-4.09250.14512710.12515118X-RAY DIFFRACTION100
4.0925-4.6840.13652730.10685166X-RAY DIFFRACTION100
4.684-5.89910.16712680.12475157X-RAY DIFFRACTION100
5.8991-43.46750.15482720.14455071X-RAY DIFFRACTION99
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)
15.0683-4.41311.23265.7343-0.96361.0349-0.2176-0.14660.05050.37160.0463-0.0559-0.0439-0.0020.14830.3065-0.04210.02040.30540.01180.2306-16.7038-4.5953-39.039
24.36-2.17150.29721.6873-0.12831.26470.0754-0.07650.2417-0.32190.0356-0.25270.00810.0015-0.05660.2538-0.03880.0130.2410.00390.2176-12.5038-2.7007-46.4225
31.9999-2.48390.25734.5386-0.07950.4595-0.214-0.4510.11480.5170.26060.14640.0134-0.12290.00810.326-0.01120.01340.37460.00690.2952-20.851-10.3124-36.4128
49.5162-7.2859-0.65138.70350.91531.6709-0.1984-0.4316-0.14960.19830.19380.02640.0635-0.0269-0.02410.3551-0.04990.0160.3624-00.3013-8.1618-3.0604-32.7163
54.1422-4.9152-0.72377.82461.31840.612-0.1217-0.34340.00840.02090.26720.01980.0870.039-0.16330.2833-0.02620.0050.30620.00720.224-3.77221.5881-37.0271
68.101-4.4587-0.6885.12470.76560.8575-0.01990.1454-0.33610.1161-0.05320.27130.0701-0.1910.07810.248-0.0541-0.00330.25420.02140.2098-25.7656-14.2312-50.79
76.762-6.4148-2.33936.66362.9021.3750.330.26460.1823-0.2972-0.2752-0.1883-0.0435-0.0695-0.12010.337-0.00780.01810.30540.02320.2783-21.6859-8.4776-56.0721
84.1033-1.97123.06374.0119-2.54643.6187-0.0322-0.38050.00140.42730.0156-0.1174-0.0517-0.3005-0.02940.3246-0.04410.05960.3664-0.02420.3282-31.7707-6.4686-41.0574
91.0682-1.42-0.93512.03980.43751.7807-0.256-0.545-0.89290.52090.11570.47980.30650.14950.32510.3659-0.05650.01260.38920.07490.4965-22.8898-25.2691-47.3105
102.2669-0.2824-0.36352.61090.27651.0744-0.1392-0.0565-0.76220.21580.06080.7750.002-0.10160.09620.3-0.06250.0020.3383-0.00070.2698-33.8991-16.1506-57.6293
112.924-3.4251-1.34476.21981.6722.1616-0.0883-0.1546-0.0654-0.07480.12410.09690.1985-0.0955-0.00630.3314-0.0731-0.01810.3286-0.00450.2868-31.3018-13.4629-64.3551
124.02222.02963.44632.37382.04715.27470.18140.0587-0.25230.11820.0945-0.14180.28730.2505-0.36040.25260.0275-0.00740.20090.0220.271912.8477-21.1036-62.1713
135.1315.91785.6346.25655.80245.80780.1343-0.01850.15660.1226-0.14780.0960.2545-0.00250.06940.24410.0002-0.01020.22480.01350.2778.1261-13.6277-62.6339
142.57112.15591.74211.690.93272.866-0.08130.14-0.217-0.18390.1006-0.09120.27550.1719-0.05350.34880.0515-0.00650.3235-0.02270.37919.537-23.8635-64.0726
158.08776.07563.68288.17983.95462.44290.4732-0.2325-0.08890.5213-0.272-0.06060.7548-0.178-0.15340.26350.03610.03080.19050.0310.274910.429-23.1692-51.9653
168.25134.89234.16264.76493.0353.37510.0783-0.0828-0.13390.1468-0.092-0.04010.19350.01620.0270.25820.00880.02080.23880.00730.25464.1475-18.8794-50.736
174.47542.41992.38622.89351.75834.44780.04310.03090.14370.0002-0.07150.21210.0175-0.18640.07390.20280.04260.03890.23130.01050.2378-32.681924.353-62.3006
187.08423.53056.07722.46073.50924.78250.21240.02-0.12310.1239-0.0345-0.01790.2126-0.0498-0.30930.25590.02380.02280.2589-0.0070.266-26.429118.3648-64.2628
192.88223.79380.57567.05971.6043.3274-0.00270.12350.2986-0.43370.01150.2337-0.4356-0.35070.07630.29660.0458-0.04780.4015-0.01070.3216-38.685527.3057-74.3492
201.6153-0.75592.64642.5148-1.47654.0095-0.0948-0.25280.44290.1691-0.2620.0415-0.565-0.39010.52240.38690.03540.05110.3901-0.05710.3955-32.99733.2718-54.3185
215.27623.74995.23072.75244.18235.95410.18-0.16620.11510.2738-0.24790.36870.2706-0.4760.27990.3352-0.00390.00340.37410.00290.3774-39.34417.3624-57.7296
223.33981.74623.89431.48742.59875.1275-0.04860.0073-0.0454-0.00330.03250.0482-0.1225-0.19780.00880.30290.0150.01780.3063-0.00130.3086-35.093911.009-56.6338
230.70370.4568-0.83591.7168-3.04157.7985-0.0480.02310.03470.0328-0.0317-0.09150.09420.14790.14180.2814-0.0107-0.02050.2907-0.03080.294717.487316.6152-48.0089
244.65362.2687-3.60413.0907-2.7814.492-0.20680.2947-0.2439-0.1141-0.0306-0.14310.1337-0.2480.20840.2013-0.0077-0.04510.2576-0.02750.233611.315312.6533-52.0604
251.60230.4257-1.77561.0592-0.66373.32820.0295-0.27310.14830.102-0.0519-0.2626-0.16030.42120.0250.3333-0.031-0.05350.34580.0070.367818.367221.6424-42.0554
268.04983.9487-5.60052.842-2.36816.31020.066-0.275-0.24430.2567-0.3285-0.3207-0.03830.56380.13550.31230.0435-0.05560.2801-0.05550.320921.76957.223-43.8201
275.6891.2904-5.4241.4074-1.53987.98230.0434-0.1489-0.21770.1082-0.1303-0.1140.01770.31420.12980.2482-0.0093-0.03920.2386-0.02530.278919.20082.1204-48.991
283.97313.5176-3.12765.3239-3.95074.78290.1122-0.07560.22890.2521-0.02980.1495-0.22850.0088-0.03670.2695-0.0112-0.03750.2736-0.03650.26314.922128.8562-46.9874
294.81445.4858-4.68955.7359-5.54234.3596-0.13370.3676-0.0715-0.13210.19180.03190.0933-0.285-0.05050.3249-0.0566-0.0090.3549-0.03990.29642.179523.8243-53.6952
301.8485-1.35160.08523.4046-3.64129.0603-0.0048-0.01990.24030.2895-0.02830.0224-0.2080.24840.03410.2969-0.07850.00560.3161-0.01520.375518.185431.5249-49.8654
319.43394.0826-2.82821.7881-1.06681.45150.1246-0.7520.2330.1203-0.05370.1771-0.13160.15-0.29410.4506-0.0131-0.00310.343-0.05390.36982.102728.865-35.2296
325.68455.7289-5.51447.0188-5.94666.76770.1948-0.02360.39690.1970.0310.155-0.54190.1943-0.20320.3578-0.0203-0.03360.3003-0.01560.3398-0.058937.8848-50.2887
337.48962.1002-6.17941.4641-2.2697.41520.125-0.1113-0.07920.1206-0.1988-0.1891-0.43950.20470.02040.2958-0.0227-0.0440.236-0.00380.2668-3.060134.4618-57.7059
344.41510.5894-5.41832.94480.02976.91390.4424-0.32570.85871.2292-0.04090.7693-1.7614-0.2485-0.40770.46240.0126-0.0370.2964-0.08020.4201-14.171437.6343-46.0854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 94 )
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 156 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 38 )
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 66 )
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 81 )
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 94 )
10X-RAY DIFFRACTION10chain 'B' and (resid 95 through 123 )
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 156 )
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 38 )
13X-RAY DIFFRACTION13chain 'C' and (resid 39 through 66 )
14X-RAY DIFFRACTION14chain 'C' and (resid 67 through 94 )
15X-RAY DIFFRACTION15chain 'C' and (resid 95 through 123 )
16X-RAY DIFFRACTION16chain 'C' and (resid 124 through 156 )
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 38 )
18X-RAY DIFFRACTION18chain 'D' and (resid 39 through 66 )
19X-RAY DIFFRACTION19chain 'D' and (resid 67 through 81 )
20X-RAY DIFFRACTION20chain 'D' and (resid 82 through 94 )
21X-RAY DIFFRACTION21chain 'D' and (resid 95 through 123 )
22X-RAY DIFFRACTION22chain 'D' and (resid 124 through 156 )
23X-RAY DIFFRACTION23chain 'E' and (resid 7 through 38 )
24X-RAY DIFFRACTION24chain 'E' and (resid 39 through 66 )
25X-RAY DIFFRACTION25chain 'E' and (resid 67 through 94 )
26X-RAY DIFFRACTION26chain 'E' and (resid 95 through 123 )
27X-RAY DIFFRACTION27chain 'E' and (resid 124 through 156 )
28X-RAY DIFFRACTION28chain 'F' and (resid 6 through 38 )
29X-RAY DIFFRACTION29chain 'F' and (resid 39 through 66 )
30X-RAY DIFFRACTION30chain 'F' and (resid 67 through 81 )
31X-RAY DIFFRACTION31chain 'F' and (resid 82 through 94 )
32X-RAY DIFFRACTION32chain 'F' and (resid 95 through 123 )
33X-RAY DIFFRACTION33chain 'F' and (resid 124 through 149 )
34X-RAY DIFFRACTION34chain 'F' and (resid 150 through 156 )

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