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- PDB-3md9: Structure of apo form of a periplasmic heme binding protein -

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Basic information

Entry
Database: PDB / ID: 3md9
TitleStructure of apo form of a periplasmic heme binding protein
ComponentsHemin-binding periplasmic protein hmuT
KeywordsTRANSPORT PROTEIN / alpha beta protein / rigid helical backbone / substrate-free / heme transport / Iron transport
Function / homology
Function and homology information


: / monoatomic ion transport / periplasmic space
Similarity search - Function
ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Hemin-binding periplasmic protein HmuT
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMattle, D. / Goetz, B.A. / Locher, K.P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Two stacked heme molecules in the binding pocket of the periplasmic heme-binding protein HmuT from Yersinia pestis.
Authors: Mattle, D. / Zeltina, A. / Woo, J.S. / Goetz, B.A. / Locher, K.P.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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: Hemin-binding periplasmic protein hmuT
B: Hemin-binding periplasmic protein hmuT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,68211
Polymers53,9342
Non-polymers7479
Water9,674537
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A: Hemin-binding periplasmic protein hmuT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2995
Polymers26,9671
Non-polymers3324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemin-binding periplasmic protein hmuT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3836
Polymers26,9671
Non-polymers4165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.710, 66.740, 62.270
Angle α, β, γ (deg.)90.00, 110.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemin-binding periplasmic protein hmuT


Mass: 26967.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: hmuT, YPO0281, y0541, YP_0436 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56991
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 29% (w/v) PEG 5K MME, 0.1 M Magnesium acetate, 0.1 MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9191 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.48→29.13 Å / Num. all: 78325 / Num. obs: 78325 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 14.24
Reflection shellResolution: 1.48→1.52 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.31 / % possible all: 97

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MD8

3md8
PDB Unreleased entry


Resolution: 1.5→29.125 Å / SU ML: 0.17 / σ(F): 1.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 5289 7.05 %Random
Rwork0.1521 ---
obs0.1541 75064 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.718 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.757 Å2-0 Å20.567 Å2
2---1.166 Å2-0 Å2
3---0.408 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 18 537 4285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093791
X-RAY DIFFRACTIONf_angle_d1.1955145
X-RAY DIFFRACTIONf_dihedral_angle_d14.6511412
X-RAY DIFFRACTIONf_chiral_restr0.073622
X-RAY DIFFRACTIONf_plane_restr0.005668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.21772080.18092313X-RAY DIFFRACTION100
1.517-1.53490.20351860.16942271X-RAY DIFFRACTION99
1.5349-1.55360.22611870.16752306X-RAY DIFFRACTION100
1.5536-1.57330.192060.16452322X-RAY DIFFRACTION99
1.5733-1.5940.19611630.1552327X-RAY DIFFRACTION99
1.594-1.61580.18731640.15062308X-RAY DIFFRACTION99
1.6158-1.63890.18151730.15112339X-RAY DIFFRACTION99
1.6389-1.66330.17391730.14732315X-RAY DIFFRACTION99
1.6633-1.68930.19031910.14572301X-RAY DIFFRACTION99
1.6893-1.7170.18181630.15142349X-RAY DIFFRACTION99
1.717-1.74660.18151880.14142279X-RAY DIFFRACTION99
1.7466-1.77840.18221950.1432273X-RAY DIFFRACTION98
1.7784-1.81260.18321850.14792300X-RAY DIFFRACTION99
1.8126-1.84960.17661860.14342246X-RAY DIFFRACTION98
1.8496-1.88980.16811530.13962374X-RAY DIFFRACTION99
1.8898-1.93370.17261790.13332352X-RAY DIFFRACTION100
1.9337-1.98210.15831570.13852337X-RAY DIFFRACTION100
1.9821-2.03570.13521910.13772322X-RAY DIFFRACTION100
2.0357-2.09560.15461900.12772317X-RAY DIFFRACTION100
2.0956-2.16320.15271740.13552357X-RAY DIFFRACTION100
2.1632-2.24050.15841480.13352338X-RAY DIFFRACTION99
2.2405-2.33010.18451920.13842318X-RAY DIFFRACTION99
2.3301-2.43610.18811400.15132348X-RAY DIFFRACTION99
2.4361-2.56450.17981530.15372329X-RAY DIFFRACTION98
2.5645-2.72510.19251590.15732303X-RAY DIFFRACTION98
2.7251-2.93530.18061820.15652369X-RAY DIFFRACTION100
2.9353-3.23030.17381730.15582342X-RAY DIFFRACTION100
3.2303-3.6970.1671760.14322365X-RAY DIFFRACTION100
3.697-4.65470.16821530.14352371X-RAY DIFFRACTION99
4.6547-29.13050.212010.18452384X-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)
10.0225-0.03570.05160.0441-0.00970.03240.1724-0.1858-0.22480.0688-0.06980.28120.13630.07-00.1175-0.0271-0.04070.1480.0040.2309-32.0673-19.6372-14.2192
20.2482-0.41020.23720.2599-0.10260.1720.0274-0.0131-0.0731-0.0582-0.02890.04260.06510.0761-00.1249-0.0094-0.01050.1245-0.00420.139-24.1668-22.4689-13.1353
30.01590.00330.00420.00280.03290.0271-0.13110.1857-0.2965-0.4422-0.3157-0.57890.19450.2807-00.28740.04760.03760.2193-0.05910.3033-18.342-26.0539-18.3275
40.05360.1199-0.0230.07840.0804-0.07980.1810.4347-0.0004-0.152-0.1038-0.45770.11980.4011-00.23160.0391-0.02440.2540.0170.1882-22.1527-13.3643-20.3336
50.2308-0.0786-0.10680.23730.17190.27820.11480.02720.0418-0.23580.13320.30890.0829-0.40420.02590.15530.0123-0.06240.21420.03340.1628-33.8045-13.4685-19.2627
60.0848-0.09450.08820.043-0.32750.1894-0.0951-0.26780.10490.0730.0519-0.0325-0.1374-0.0689-00.12550.0264-0.03040.14350.01040.1579-29.2313-8.0833-11.2796
70.0053-0.139-0.14660.6038-0.28450.19340.048-0.29980.0810.0794-0.053-0.2271-0.14830.0152-00.0906-0.00620.00220.13740.01090.1157-20.4241-16.7792-0.3988
80.0263-0.0052-0.0123-0.0029-0.01630.03010.0529-0.4407-0.66070.02730.24160.22750.2579-0.513200.1555-0.0665-0.05950.33590.07020.2288-31.6062-26.1789-0.3111
90.2009-0.2222-0.01190.08210.0740.28360.0225-0.449-0.29330.1015-0.0697-0.04680.1089-0.0861-0.00010.1371-0.00970.00090.14650.0720.1811-15.1601-27.42413.3325
100.61720.47140.33910.5181-0.01791.34590.0081-0.18040.02420.1359-0.1237-0.0307-0.1731-0.0927-0.64460.0747-0.0198-0.00470.10780.00940.06613.2607-14.3713-3.0676
110.18050.12170.26720.24710.10430.4960.03710.27670.0689-0.2081-0.47070.2497-0.1258-0.0736-0.03840.18460.0997-0.02370.1812-0.01970.1321-2.4295-4.7963-17.5866
121.04480.09380.21790.18790.00870.1380.219-0.29340.07840.1656-0.17660.1049-0.0834-0.03440.03450.133-0.0240.03070.1163-0.01830.0963-1.326-9.2944-2.0845
130.0345-0.1280.16060.1075-0.08860.22490.22850.11040.3128-0.1254-0.10610.1278-0.1043-0.1101-00.1268-0.00610.02390.1076-0.01860.15162.5275-1.0388-11.5799
140.2024-0.1168-0.21570.1616-0.04440.19640.0708-0.0450.04340.0786-0.06850.0058-0.01830.0018-0.00390.0831-0.0082-0.00080.06690.00060.06977.0807-10.9119-9.8294
150.026-0.08-0.11110.33210.16710.48450.04490.21640.0473-0.1743-0.01260.3734-0.0542-0.4259-0.01920.13440.0225-0.01670.12770.00210.1179-2.755-14.2325-22.3993
160.10250.11080.0463-0.0202-0.03620.06660.0043-0.01370.0445-0.0556-0.0569-0.07050.00530.0032-00.11380.00190.00950.0924-0.00430.09410.0626-11.4536-18.0125
170.29610.0027-0.00810.0520.04410.033-0.143-0.4286-0.07840.02720.0419-0.14930.08950.1487-0.00140.08470.00380.00040.1111-0.00550.124311.4346-18.4969-13.0752
180.3001-0.1211-0.22340.12630.1860.18850.0820.26670.0313-0.10710.04510.0289-0.053-0.18470.0080.0795-0.0032-0.00770.12750.01220.1148-9.317-18.721-10.3987
190.0645-0.0198-0.06260.02370.03940.05080.00820.2381-0.3661-0.1537-0.04460.12270.0690.0777-00.12450.0045-0.00880.12830.00820.1427-5.6884-24.2691-4.9357
200.04590.0115-0.00970.00820.35280.25830.03850.035-0.08930.02990.1648-0.4317-0.05841.10320.14730.11620.0178-0.00370.3265-0.01130.12656.3289-24.1578-3.4081
210.02890.14190.02220.15280.23080.28830.2877-0.45340.59590.0657-0.1270.34220.09220.02610.00330.12330.0260.05990.2788-0.08820.3732-14.9826-9.9032-41.7093
220.32850.1151-0.00750.0981-0.03820.05590.2552-0.58240.50630.1868-0.27520.3461-0.1025-0.01160.04730.16810.01480.06540.272-0.14210.3983-13.0227-7.4432-39.3176
230.00890.0064-0.00360.00530.00780.01960.0936-0.45960.21090.2806-0.1582-0.0298-0.2369-0.06800.36-0.04830.07490.6787-0.38280.4709-9.4165-7.2561-31.2733
240.2292-0.07280.75630.07760.24791.52790.1055-0.80020.01620.1795-0.0678-0.27350.5823-0.1720.04880.1474-0.03880.13990.6305-0.21820.3879-18.2163-13.2322-32.5095
25-0.016-0.0205-0.01030.0016-0.03650.06890.1921-0.8991-0.04160.5053-0.31130.34120.0279-0.2743-00.2402-0.03430.09820.5190.02720.4604-24.9577-17.2589-37.4656
260.11750.02460.0160.01790.02180.12710.009-0.0366-0.0446-0.10250.0820.15930.105-0.32780.00230.09310.0170.00710.25570.00610.2904-18.3581-14.9819-44.4709
270.0645-0.0298-0.06840.10470.09160.08980.02760.5467-0.3025-0.1016-0.41050.41910.244-0.0286-0.00070.1641-0.0122-0.0170.4084-0.03420.4415-24.9143-20.1635-46.1924
280.27360.39590.06040.33610.12670.0710.13890.1631-0.02720.014-0.12630.08410.1874-0.11490.00070.11160.0003-0.00650.18040.01210.1379-6.1004-16.8351-48.1235
290.0575-0.00770.02520.09030.05140.19130.00030.51610.6599-0.20460.03640.27-0.3122-0.20570.010.18710.0528-0.04070.21340.09090.3118-4.1871-4.3376-52.9003
300.0692-0.00630.00690.0046-0.03840.13090.12520.06830.0591-0.0261-0.057-0.1107-0.18530.15730.00040.1512-0.0084-0.01130.11160.00530.10537.6346-12.1779-45.1663
310.0918-0.1910.1020.51850.05160.2703-0.1470.16980.0939-0.05110.0565-0.0103-0.0031-0.0392-0.00120.0802-0.00150.00320.10410.00950.08929.2151-28.8462-31.8128
320.15390.1145-0.1524-0.4457-0.3244-0.0072-0.1613-0.2281-0.09510.4016-0.10510.81970.0539-0.4566-0.06980.1844-0.02950.14710.2358-0.05160.3094-6.8537-35.7183-23.8814
330.7164-0.14780.10220.6146-0.1650.4948-0.01220.04660.0041-0.0571-0.0211-0.00330.0703-0.0411-0.30390.1035-0.00840.00540.0786-0.01760.0734.3614-32.7135-35.8845
340.1349-0.00630.05990.04-0.06020.2278-0.0485-0.0042-0.08160.05930.0156-0.00650.0904-0.0145-0.02780.1230.00130.00820.0693-0.00740.09695.7241-36.7752-24.723
350.00690.0465-0.1359-0.0126-0.03790.29680.03620.11060.09980.1492-0.04540.2512-0.1711-0.51980.00240.1154-0.01810.01220.1426-0.01150.1107-5.239-24.3287-21.1441
360.2797-0.6427-0.0411.01090.27320.3629-0.11060.0112-0.03850.2954-0.02370.10020.2107-0.0312-0.08390.17090.01240.01350.081-0.0060.09415.7939-32.3278-16.5426
370.2875-0.0354-0.04440.11460.14430.0902-0.2208-0.00890.07270.16890.0571-0.1703-0.0381-0.0056-0.01080.12280.0138-0.01740.07440.00340.10719.6807-25.0331-20.2298
380.0136-0.03710.02250.05810.04510.0793-0.14440.01020.05080.0316-0.04230.29990.2283-0.515-0.00220.1040.008-0.01340.17260.00330.13-2.4468-19.4158-30.7313
390.33810.05730.19960.1787-0.21770.3209-0.0579-0.15450.189-0.00440.01-0.0379-0.0558-0.115-0.00060.125-0.0096-0.00350.102-0.01590.09174.6007-17.4455-35.7524
400.13550.4646-0.25630.2947-0.17770.4494-0.0139-0.1288-0.27380.46250.1108-0.66620.17390.8352-0.05610.1963-0.0226-0.09130.2171-0.01060.181316.0083-21.1199-27.8161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 26:32)A26 - 32
2X-RAY DIFFRACTION2(chain A and resid 33:56)A33 - 56
3X-RAY DIFFRACTION3(chain A and resid 57:63)A57 - 63
4X-RAY DIFFRACTION4(chain A and resid 64:75)A64 - 75
5X-RAY DIFFRACTION5(chain A and resid 76:86)A76 - 86
6X-RAY DIFFRACTION6(chain A and resid 87:111)A87 - 111
7X-RAY DIFFRACTION7(chain A and resid 112:131)A112 - 131
8X-RAY DIFFRACTION8(chain A and resid 132:136)A132 - 136
9X-RAY DIFFRACTION9(chain A and resid 137:153)A137 - 153
10X-RAY DIFFRACTION10(chain A and resid 154:165)A154 - 165
11X-RAY DIFFRACTION11(chain A and resid 166:176)A166 - 176
12X-RAY DIFFRACTION12(chain A and resid 177:198)A177 - 198
13X-RAY DIFFRACTION13(chain A and resid 199:206)A199 - 206
14X-RAY DIFFRACTION14(chain A and resid 207:219)A207 - 219
15X-RAY DIFFRACTION15(chain A and resid 220:227)A220 - 227
16X-RAY DIFFRACTION16(chain A and resid 228:244)A228 - 244
17X-RAY DIFFRACTION17(chain A and resid 245:250)A245 - 250
18X-RAY DIFFRACTION18(chain A and resid 251:262)A251 - 262
19X-RAY DIFFRACTION19(chain A and resid 263:271)A263 - 271
20X-RAY DIFFRACTION20(chain A and resid 272:278)A272 - 278
21X-RAY DIFFRACTION21(chain B and resid 26:38)B26 - 38
22X-RAY DIFFRACTION22(chain B and resid 39:56)B39 - 56
23X-RAY DIFFRACTION23(chain B and resid 57:63)B57 - 63
24X-RAY DIFFRACTION24(chain B and resid 64:71)B64 - 71
25X-RAY DIFFRACTION25(chain B and resid 72:82)B72 - 82
26X-RAY DIFFRACTION26(chain B and resid 83:93)B83 - 93
27X-RAY DIFFRACTION27(chain B and resid 94:108)B94 - 108
28X-RAY DIFFRACTION28(chain B and resid 109:132)B109 - 132
29X-RAY DIFFRACTION29(chain B and resid 133:140)B133 - 140
30X-RAY DIFFRACTION30(chain B and resid 141:153)B141 - 153
31X-RAY DIFFRACTION31(chain B and resid 154:166)B154 - 166
32X-RAY DIFFRACTION32(chain B and resid 167:174)B167 - 174
33X-RAY DIFFRACTION33(chain B and resid 175:200)B175 - 200
34X-RAY DIFFRACTION34(chain B and resid 201:218)B201 - 218
35X-RAY DIFFRACTION35(chain B and resid 219:227)B219 - 227
36X-RAY DIFFRACTION36(chain B and resid 228:245)B228 - 245
37X-RAY DIFFRACTION37(chain B and resid 246:251)B246 - 251
38X-RAY DIFFRACTION38(chain B and resid 252:257)B252 - 257
39X-RAY DIFFRACTION39(chain B and resid 258:272)B258 - 272
40X-RAY DIFFRACTION40(chain B and resid 273:278)B273 - 278

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