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- PDB-5kob: Crystal structure of a peptide deformylase from Burkholderia xeno... -

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Basic information

Entry
Database: PDB / ID: 5kob
TitleCrystal structure of a peptide deformylase from Burkholderia xenovorans
ComponentsPeptide deformylase
KeywordsHYDROLASE / SSGCID / peptide deformylase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / translation / metal ion binding
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / FORMIC ACID / Peptide deformylase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a peptide deformylase from Burkholderia xenovorans
Authors: Mayclin, S.J. / Conrady, D.G. / Edwards, T.E. / Staker, B. / Myler, P. / Stewart, L.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase
B: Peptide deformylase
C: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,28535
Polymers83,7714
Non-polymers1,51431
Water12,268681
1
A: Peptide deformylase
C: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,68819
Polymers41,8862
Non-polymers80217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-48 kcal/mol
Surface area15640 Å2
MethodPISA
2
B: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,59816
Polymers41,8862
Non-polymers71214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-42 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.550, 92.000, 142.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peptide deformylase / PDF / Polypeptide deformylase


Mass: 20942.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: def, Bxe_A1677 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13XB1, peptide deformylase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.61 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ A5 (270125a5): 20% w/v PEG3350, 200mM Magnesium formate dihydrate; 20eg2step; protein 22mg/mL; ehj6-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 31, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 109668 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 20.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.52
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.6-1.645.50.5082.890.8921100
1.64-1.690.4143.550.925199.9
1.69-1.740.3374.40.9461100
1.74-1.790.2695.480.9641100
1.79-1.850.2057.120.9761100
1.85-1.910.1658.880.986199.9
1.91-1.980.12611.410.991199.9
1.98-2.070.114.320.994199.7
2.07-2.160.08217.450.995199.8
2.16-2.260.07120.450.996199.7
2.26-2.390.06123.280.997199.4
2.39-2.530.05525.740.998199.3
2.53-2.70.04928.880.998199.1
2.7-2.920.04331.990.998198.8
2.92-3.20.03835.330.998198.6
3.2-3.580.03538.690.998198.3
3.58-4.130.03241.090.999198
4.13-5.060.03141.890.999197.4
5.06-7.160.03141.40.999196.1
7.16-500.03239.560.998190.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIX(dev_2443: ???)refinement
PDB_EXTRACT3.2data extraction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GHW
Resolution: 1.6→49.072 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.78
RfactorNum. reflection% reflection
Rfree0.1919 1931 1.76 %
Rwork0.1647 --
obs0.1652 109637 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 30.2831 Å2 / Biso min: 13.22 Å2
Refinement stepCycle: final / Resolution: 1.6→49.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 88 684 5909
Biso mean--52.14 38.74 -
Num. residues----659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065528
X-RAY DIFFRACTIONf_angle_d0.8737510
X-RAY DIFFRACTIONf_chiral_restr0.061816
X-RAY DIFFRACTIONf_plane_restr0.007994
X-RAY DIFFRACTIONf_dihedral_angle_d13.4513327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.25571340.228476287762100
1.64-1.68440.22061420.206576077749100
1.6844-1.73390.21561640.191176667830100
1.7339-1.78990.20461240.179676587782100
1.7899-1.85390.20641270.175176957822100
1.8539-1.92810.22411450.176577067851100
1.9281-2.01590.24241470.171476297776100
2.0159-2.12210.18191490.167877117860100
2.1221-2.25510.19351410.167977007841100
2.2551-2.42920.1941140.1687727784199
2.4292-2.67370.2121250.17437690781599
2.6737-3.06050.22131350.17497723785899
3.0605-3.85570.16841430.15447747789098
3.8557-49.09490.1651410.14337819796096
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)
16.2293-1.9185-5.28793.08254.19299.1066-0.1529-0.18670.16170.5107-0.01540.5303-0.6364-0.58630.13920.3720.06330.06290.2114-0.01230.2488-24.032310.61573.3673
27.62792.8622-5.22354.1348-3.12683.9813-0.2146-0.4809-0.33590.1023-0.1887-0.07750.30520.20520.53190.2233-0.00520.01620.1596-0.00060.1181-19.1866-4.326111.3031
34.1267-1.92662.55845.6486-4.55013.9819-0.1008-0.1520.19870.41130.11370.2241-0.5137-0.716-0.0240.21950.02320.06630.2774-0.02970.2068-31.92312.631711.1215
41.24460.2389-0.45862.4366-0.262.1361-0.04550.217-0.024-0.1024-0.03630.40510.2456-0.58110.06790.1841-0.04190.01670.2714-0.02860.1814-31.0492-3.2544-0.2949
52.8994-0.60190.23934.2901-3.51584.0964-0.07810.346-0.402-0.3036-0.23860.00550.9367-0.15980.17940.3151-0.06150.05780.1939-0.03180.1987-25.9175-11.135-14.7655
61.78551.1094-0.13743.6549-0.25663.5890.01650.03920.02980.0802-0.00690.11610.1541-0.33870.00840.0991-0.0080.0170.1402-0.00090.1134-26.31071.2136-10.9545
70.6524-0.02670.29870.9-1.82623.84620.0520.0231-0.10920.3911-0.03820.29351.4828-0.59640.07790.4073-0.14710.07480.2197-0.01150.2582-28.77-14.07745.1517
82.36750.0380.12661.2098-0.94983.2764-0.061-0.0269-0.14690.09020.0130.18530.3381-0.38770.00640.2338-0.03930.06230.1342-0.0150.1581-27.8602-9.396-2.837
92.66481.04792.36953.8185-0.48692.75050.10680.2228-0.09090.14010.0427-0.06790.3950.7295-0.13010.19870.02810.00970.2062-0.0070.1529-18.7455-0.5145-12.1284
104.3631-0.11140.25236.32771.28768.6937-0.01950.14420.2846-0.10860.07360.5913-0.2565-0.5649-0.06610.1265-0.00970.00030.210.04080.2051-28.84756.727-19.4195
116.76622.4858-3.09465.9968-2.27986.20430.1187-0.4446-0.34180.1167-0.25160.07820.2483-0.30220.12950.1526-0.0326-0.00210.24290.01120.1732-26.7124-5.426-34.7152
122.4873-1.26310.89285.4478-1.50611.5599-0.1787-0.4878-0.06640.57790.0882-0.13720.00810.06620.12220.24360.01620.00660.28740.01140.1138-12.7607-4.2014-22.7672
136.43250.84764.4663.63722.49427.12890.2569-0.4096-0.7471-0.14590.25310.47191.2733-0.5835-0.41640.4748-0.061-0.03180.20690.11820.3427-20.3152-16.4088-26.4969
144.5339-0.8353-0.34825.00191.07823.64260.03770.2699-0.7622-0.2628-0.0291-0.02290.6622-0.00950.04320.28420.01810.00710.1573-0.02490.1983-15.5806-13.8396-34.0158
154.7389-0.0007-0.82752.5770.49912.81240.029-0.1849-0.01670.22230.0324-0.10480.20930.231-0.06650.22580.0764-0.00630.2296-0.00470.1467-5.5137-8.6157-32.5079
169.77120.5904-0.06240.7326-0.3131.0475-0.05320.2987-0.1183-0.06360.0216-0.06850.25160.17970.05430.24280.0480.00010.1732-0.00780.1527-12.8818-9.0943-48.4932
174.66791.8069-5.77251.6581-2.73788.14070.0202-0.6814-0.24230.1959-0.06670.06150.10751.1840.15280.28080.1611-0.00240.27530.03490.1947-3.8074-12.5353-30.5652
182.2016-0.30180.90920.87630.21683.6978-0.1228-0.1079-0.16880.03370.06210.01780.10320.21410.05980.14150.02740.01290.17420.00710.1244-10.4175-8.3363-41.5358
199.57633.1569-3.02316.216-1.53586.0962-0.0780.3722-0.6092-0.11420.1940.1540.823-0.2261-0.14680.28560.0123-0.06410.1705-0.02740.1975-23.3839-11.1395-55.9815
203.7165-1.59111.06414.98750.06477.3616-0.11360.45580.5166-0.33530.28240.2482-0.4103-0.5451-0.14530.1254-0.0142-0.02540.27950.10530.2966-27.101115.1711-26.7223
211.91670.6719-1.43242.1768-1.84962.3522-0.13930.40630.4058-0.55230.36210.4103-0.4704-0.14-0.20210.3306-0.09-0.05410.280.10810.2756-19.222523.8683-32.8836
227.18553.2851-5.56236.1889-3.18856.48790.2017-0.47790.07450.4673-0.20270.1132-0.61490.6558-0.04290.3222-0.13310.03080.2326-0.01580.2277-10.518826.5223-17.2302
234.2412.33312.31153.6171-1.52275.0305-0.23910.58750.0327-0.62390.28830.0664-0.19080.60950.0090.2233-0.15850.0390.3318-0.00470.1565-8.118320.6128-34.1517
249.3777-1.5026-6.07821.79630.853.9764-0.1256-0.3379-0.24040.07580.1766-0.56080.28491.10160.00420.16520.03950.01630.4946-0.02780.3472-1.974412.297-19.8249
251.80591.1968-0.76042.0267-0.89142.3701-0.03910.21020.0586-0.33750.2038-0.1242-0.23660.4209-0.12590.2059-0.06860.02830.2624-0.01740.1869-10.069718.6969-27.0243
263.08661.5066-1.4592.62880.05462.0494-0.06540.0839-0.0359-0.12780.1533-0.1782-0.17910.5178-0.00240.1253-0.04970.00450.251-0.00280.1566-9.895814.6935-24.8771
277.36472.98682.80043.54355.50659.3895-0.1482-0.32630.66590.02410.28310.2063-0.81140.3155-0.14770.2989-0.02840.03680.1764-0.01340.2276-16.91917.2553-6.8271
286.8192.48290.0674.53911.86774.94090.10270.2515-0.0775-0.26730.02030.47430.6288-0.348-0.11740.2607-0.025-0.08380.14410.00270.2294-31.3702-8.7585-63.3308
294.4563-0.63252.74131.7008-0.73482.53240.46120.9965-0.2916-0.4551-0.17160.20710.55390.1008-0.23540.35190.0353-0.08990.4266-0.03290.208-33.2202-0.3335-78.5423
304.4461-0.79853.02793.0109-1.81367.92210.1362-0.2409-0.6752-0.3210.38740.99290.6574-1.1281-0.36510.3001-0.1088-0.16640.470.08910.5637-44.6529-3.1963-70.5676
315.664-0.14610.70545.4039-2.87638.29360.1764-0.0678-0.09170.09140.1850.4140.1614-0.337-0.23740.2274-0.0196-0.07130.16180.01160.2239-36.1178-2.1654-67.0481
322.2687-2.981-3.07884.07013.84614.5037-0.0297-0.1897-0.17150.1234-0.12420.78840.3296-1.11080.17510.1790.0369-0.02640.45440.00450.341-41.93457.4167-65.6774
333.6787-0.4649-0.17313.16290.05524.5466-0.00860.26870.2512-0.10990.06780.0014-0.3589-0.0791-0.03030.19960.0463-0.03430.22660.02530.2251-33.485410.5718-71.5791
347.65984.644-4.09894.6061-0.59774.26420.3108-0.31720.48760.2677-0.21760.2225-0.92040.5643-0.03680.3716-0.0368-0.06280.2331-0.02680.2852-27.392115.4428-55.3984
351.8907-0.0737-0.08146.4154-3.17976.7617-0.0505-0.09030.06570.005-0.01880.1377-0.1221-0.24320.04570.1190.0194-0.02950.1782-0.02270.1688-30.64523.2913-54.0867
363.96051.63351.8175.8113.92757.141-0.20480.44680.4223-0.45140.15530.4195-0.7472-0.26630.04030.31920.0788-0.08050.24010.07740.2928-37.234713.0971-73.0975
372.1482-0.70270.90922.9692-1.41954.8557-0.0144-0.03990.16920.04350.07030.1655-0.3475-0.3018-0.06640.16560.0102-0.03060.1405-0.00710.1783-30.8858.7419-62.0551
382.41222.0002-3.21229.78670.17465.55350.3119-0.3050.08810.6052-0.12260.5607-0.3312-0.6402-0.19880.23910.0459-0.01030.33750.00780.2118-30.41241.0081-43.9072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 13 )A0 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 25 )A14 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 41 )A26 - 41
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 87 )A42 - 87
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 97 )A88 - 97
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 112 )A98 - 112
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 125 )A113 - 125
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 147 )A126 - 147
9X-RAY DIFFRACTION9chain 'A' and (resid 148 through 157 )A148 - 157
10X-RAY DIFFRACTION10chain 'A' and (resid 158 through 169 )A158 - 169
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 14 )B1 - 14
12X-RAY DIFFRACTION12chain 'B' and (resid 15 through 25 )B15 - 25
13X-RAY DIFFRACTION13chain 'B' and (resid 26 through 42 )B26 - 42
14X-RAY DIFFRACTION14chain 'B' and (resid 43 through 77 )B43 - 77
15X-RAY DIFFRACTION15chain 'B' and (resid 78 through 87 )B78 - 87
16X-RAY DIFFRACTION16chain 'B' and (resid 88 through 112 )B88 - 112
17X-RAY DIFFRACTION17chain 'B' and (resid 113 through 125 )B113 - 125
18X-RAY DIFFRACTION18chain 'B' and (resid 126 through 157 )B126 - 157
19X-RAY DIFFRACTION19chain 'B' and (resid 158 through 169 )B158 - 169
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 14 )C2 - 14
21X-RAY DIFFRACTION21chain 'C' and (resid 15 through 66 )C15 - 66
22X-RAY DIFFRACTION22chain 'C' and (resid 67 through 76 )C67 - 76
23X-RAY DIFFRACTION23chain 'C' and (resid 77 through 87 )C77 - 87
24X-RAY DIFFRACTION24chain 'C' and (resid 88 through 97 )C88 - 97
25X-RAY DIFFRACTION25chain 'C' and (resid 98 through 125 )C98 - 125
26X-RAY DIFFRACTION26chain 'C' and (resid 126 through 160 )C126 - 160
27X-RAY DIFFRACTION27chain 'C' and (resid 161 through 171 )C161 - 171
28X-RAY DIFFRACTION28chain 'D' and (resid 2 through 14 )D2 - 14
29X-RAY DIFFRACTION29chain 'D' and (resid 15 through 25 )D15 - 25
30X-RAY DIFFRACTION30chain 'D' and (resid 26 through 41 )D26 - 41
31X-RAY DIFFRACTION31chain 'D' and (resid 42 through 57 )D42 - 57
32X-RAY DIFFRACTION32chain 'D' and (resid 58 through 77 )D58 - 77
33X-RAY DIFFRACTION33chain 'D' and (resid 78 through 87 )D78 - 87
34X-RAY DIFFRACTION34chain 'D' and (resid 88 through 97 )D88 - 97
35X-RAY DIFFRACTION35chain 'D' and (resid 98 through 112 )D98 - 112
36X-RAY DIFFRACTION36chain 'D' and (resid 113 through 125 )D113 - 125
37X-RAY DIFFRACTION37chain 'D' and (resid 126 through 157 )D126 - 157
38X-RAY DIFFRACTION38chain 'D' and (resid 158 through 169 )D158 - 169

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