[English] 日本語
Yorodumi
- PDB-5kob: Crystal structure of a peptide deformylase from Burkholderia xeno... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.61 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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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