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- PDB-5vrb: Crystal structure of a transketolase from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 5vrb
TitleCrystal structure of a transketolase from Neisseria gonorrhoeae
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase / TPP / thiamine / thiamine pyrophosphate / calcium-dependent / NIAID / structural genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


transketolase / transketolase activity / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 ...Transketolase, bacterial-like / Transketolase family / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a transketolase from Neisseria gonorrhoeae
Authors: Edwards, T.E. / Delker, S.L. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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.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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase
B: Transketolase
C: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,77722
Polymers290,9244
Non-polymers85318
Water36,7332039
1
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9135
Polymers72,7311
Non-polymers1824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8514
Polymers72,7311
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9756
Polymers72,7311
Non-polymers2445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0377
Polymers72,7311
Non-polymers3066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.450, 114.210, 125.690
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transketolase


Mass: 72731.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: NGK_0759 / Production host: Escherichia coli (E. coli) / References: UniProt: B4RKU9, transketolase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2039 / 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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NegoA.01294.a.B1.PS37968 at 22.9 mg/mL against MCSG1 screen condition E9 0.2 M calcium chloride, 25% PEG 3350, cryo-protected with 15% ethylene glycol, 1 mM TPP, 2 mM CaCl2, crystal tracking ...Details: NegoA.01294.a.B1.PS37968 at 22.9 mg/mL against MCSG1 screen condition E9 0.2 M calcium chloride, 25% PEG 3350, cryo-protected with 15% ethylene glycol, 1 mM TPP, 2 mM CaCl2, crystal tracking ID 282795e9, unique puck ID pap7-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→37.591 Å / Num. obs: 195499 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.152 % / Biso Wilson estimate: 18.41 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.086 / Χ2: 1.026 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.92.9350.4552.83143010.7440.55798.1
1.9-1.953.210.3753.72139950.8280.45198.2
1.95-2.013.2090.2874.77136600.8910.34598.4
2.01-2.073.2010.235.87132490.9280.27798.6
2.07-2.143.1970.1827.2128330.9530.21998.6
2.14-2.213.1970.1528.45124640.9660.18398.7
2.21-2.293.1960.139.66120420.9720.15798.8
2.29-2.393.1910.11110.94116230.980.13398.9
2.39-2.493.1930.09612.34111000.9840.11599
2.49-2.623.1850.08613.51106510.9870.10399.1
2.62-2.763.1760.07515.23101540.9890.0999.1
2.76-2.933.1660.06417.5596150.9920.07799.1
2.93-3.133.1390.05519.5590140.9930.06799.1
3.13-3.383.1270.04722.2383980.9950.05799
3.38-3.73.0970.04124.8277710.9960.04998.9
3.7-4.143.0450.03826.6469480.9960.04698.6
4.14-4.783.0970.03628.1761440.9960.04398.4
4.78-5.853.0920.03527.7352130.9960.04398.2
5.85-8.273.1160.03528.1440950.9960.04299
8.27-37.5913.0560.03130.2722290.9970.03896.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2r8o
Resolution: 1.85→37.591 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.29
RfactorNum. reflection% reflection
Rfree0.1907 1970 1.01 %
Rwork0.1505 --
obs0.1509 195491 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.72 Å2 / Biso mean: 22.416 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 1.85→37.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19017 0 36 2060 21113
Biso mean--28.49 29.94 -
Num. residues----2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619673
X-RAY DIFFRACTIONf_angle_d0.76926806
X-RAY DIFFRACTIONf_chiral_restr0.052988
X-RAY DIFFRACTIONf_plane_restr0.0053513
X-RAY DIFFRACTIONf_dihedral_angle_d11.48411631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89630.25411280.2189135981372698
1.8963-1.94750.23981310.1877137691390098
1.9475-2.00480.20631190.1729138041392398
2.0048-2.06950.21541600.1643137271388799
2.0695-2.14350.19371660.1564137191388599
2.1435-2.22930.19911600.1529137831394399
2.2293-2.33080.19991510.142138441399599
2.3308-2.45360.18481660.1417137531391999
2.4536-2.60730.1881460.146138991404599
2.6073-2.80860.18811330.145138551398899
2.8086-3.09110.20651560.151139171407399
3.0911-3.53810.16751160.1461139091402599
3.5381-4.45650.16781310.132138631399499
4.4565-37.59880.17871070.1517140811418898
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)
18.2281-2.1219-4.23023.27080.49292.29830.0991-0.05830.4287-0.0750.0360.1537-0.1015-0.1401-0.15460.1527-0.0198-0.03540.20690.02690.1642-6.6776.73064.5183
22.0583-1.1159-2.16181.80261.58663.51270.00990.0429-0.0068-0.04290.03470.1230.1371-0.1652-0.04610.1393-0.0319-0.03990.20190.02660.0976-5.5988-5.25238.2386
30.65630.13060.26151.1759-0.44510.83890.01330.0620.018-0.1572-0.0353-0.02420.0396-0.02920.02340.14440.02010.02230.16420.01150.07212.1430.35585.386
41.8515-0.4772-0.51860.26380.14611.40170.12790.2748-0.0182-0.2889-0.02810.24830.0663-0.1532-0.06990.3069-0.054-0.07880.2791-0.00630.1394-6.7738-5.2121-3.107
50.50250.13580.2340.66910.06881.39450.06140.0767-0.1267-0.122-0.0033-0.12670.32580.1311-0.05790.18420.03820.01670.119-0.00250.130919.719-17.737421.1184
60.92410.1474-0.12442.3492-0.98661.65580.0544-0.0724-0.2076-0.0418-0.0569-0.11080.25840.0116-0.00130.1348-0.0081-0.00330.10230.0180.139315.049-24.850636.2286
70.7550.5130.03791.49020.00770.8840.1093-0.2601-0.14630.2648-0.0889-0.01580.1482-0.1203-0.01410.1624-0.01490.0050.16660.04990.129816.3498-19.979149.102
80.6474-0.20060.25781.1722-0.13360.6722-0.01840.11070.1365-0.0108-0.0597-0.2172-0.02810.15270.06420.0789-0.00070.01230.14740.03290.214242.92667.747435.3621
90.8548-0.0260.13170.5392-0.04691.242-0.02420.15520.1301-0.0877-0.0505-0.1473-0.04240.13460.0480.1082-0.00370.02350.14430.05960.162232.726312.730822.7336
100.6398-0.76280.23121.0763-0.00220.6795-0.05940.08370.30830.0712-0.038-0.418-0.12860.12550.05930.1517-0.0535-0.01250.14310.02110.349941.958416.448337.9039
110.98540.01060.0191.35710.37581.1553-0.0002-0.04160.19660.0715-0.12120.1652-0.2039-0.17750.07190.1260.03910.00630.1257-0.0080.17169.660220.709736.1317
121.04030.62760.26750.90770.37270.3255-0.0566-0.01940.0193-0.04710.0260.068-0.0362-0.08360.03450.09850.01490.00920.13190.0180.09629.29526.118933.6277
131.33810.354-0.7131.2566-0.12331.46390.0832-0.20090.16050.1622-0.03660.1411-0.2022-0.179-0.0860.11840.03660.01540.1867-0.02360.1082.47737.889149.1843
140.7718-0.0718-0.16670.7940.4540.68810.0627-0.2701-0.06750.1408-0.04590.04850.0811-0.226-0.02540.1293-0.0050.02770.270.02780.1238-3.0061-2.74252.2007
150.76830.0475-0.96770.7329-0.2131.87430.0978-0.1749-0.04950.0661-0.02090.22230.1193-0.2992-0.09070.1189-0.04680.02180.27070.0050.1613-11.1688-6.028638.7109
164.2269-1.28672.68782.3811-0.90581.72050.11840.1191-0.2477-0.1135-0.0724-0.19240.26090.3204-0.0490.17140.04970.03090.2968-0.04030.21848.51012.500168.7259
171.4815-0.82921.35831.7886-1.58332.50990.01250.10650.04390.0955-0.0684-0.2527-0.07110.31930.06220.1361-0.00970.01070.1963-0.0370.140945.57314.198572.3258
181.0158-0.033-0.04732.4082-0.461.14770.08880.120.0093-0.0838-0.0392-0.0442-0.03440.1229-0.04750.12350.00570.01970.1395-0.02270.084530.695914.728671.5697
191.70540.3978-0.9311.0830.30541.5233-0.03750.1195-0.2339-0.05260.0051-0.16750.23810.08850.04830.15990.0316-0.01320.1495-0.03940.126330.6033-0.293866.5143
204.671-3.68960.48523.8477-0.98051.46730.16850.50740.3307-0.2613-0.2895-0.4191-0.03850.41570.09070.2239-0.04440.03610.3244-0.00710.150346.174518.802460.4284
210.48340.1086-0.02470.6249-0.01790.84120.06690.0320.1053-0.0281-0.02190.0944-0.1273-0.0717-0.03860.1130.0140.01020.0861-0.00480.110820.17122.661486.1857
220.5476-0.53560.02341.40340.72521.12340.2057-0.1550.31410.2661-0.04340.065-0.32960.0676-0.11810.3043-0.06970.11270.135-0.05820.214822.194732.362103.7673
230.26070.12750.07651.4056-0.03891.14150.2179-0.20910.12710.5013-0.10720.0374-0.19970.0908-0.07450.2938-0.06040.04640.1839-0.05530.140820.450322.9202112.9638
241.3459-0.5098-0.12772.16890.1710.77490.0259-0.0169-0.13750.0119-0.03770.13380.0605-0.14750.00720.1298-0.0489-0.0160.1326-0.00580.1561-1.5722-7.431495.8337
251.06490.2012-0.17750.48750.09890.90040.00410.1431-0.2355-0.0908-0.00970.03540.0781-0.08670.00270.1679-0.0186-0.03040.106-0.04480.187910.132-10.737883.6788
262.0062-0.47310.33563.6885-0.29921.94240.05270.02480.0027-0.1662-0.04990.3742-0.0493-0.32770.00680.1396-0.0305-0.04950.2257-0.04940.2906-13.2887-2.425692.5951
271.1070.2503-0.04970.62780.1270.46780.0373-0.1284-0.3670.0687-0.0272-0.13750.19150.08370.00480.19010.0164-0.03870.11010.03360.222629.0901-12.517699.5028
282.40260.38542.13831.65240.373.32360.0573-0.251-0.21390.2656-0.0379-0.26510.06530.2814-0.09880.21870.022-0.06090.22710.05510.182641.5244-2.5838114.6455
290.54760.07570.37691.0797-0.28030.8960.0247-0.1510.05670.303-0.0677-0.2046-0.18590.23720.02770.2474-0.02-0.09280.2245-0.01040.182544.14249.8307112.0365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 40 )A2 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 96 )A41 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 241 )A97 - 241
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 314 )A242 - 314
5X-RAY DIFFRACTION5chain 'A' and (resid 315 through 474 )A315 - 474
6X-RAY DIFFRACTION6chain 'A' and (resid 475 through 554 )A475 - 554
7X-RAY DIFFRACTION7chain 'A' and (resid 555 through 659 )A555 - 659
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 96 )B2 - 96
9X-RAY DIFFRACTION9chain 'B' and (resid 97 through 254 )B97 - 254
10X-RAY DIFFRACTION10chain 'B' and (resid 255 through 333 )B255 - 333
11X-RAY DIFFRACTION11chain 'B' and (resid 334 through 421 )B334 - 421
12X-RAY DIFFRACTION12chain 'B' and (resid 422 through 474 )B422 - 474
13X-RAY DIFFRACTION13chain 'B' and (resid 475 through 554 )B475 - 554
14X-RAY DIFFRACTION14chain 'B' and (resid 555 through 626 )B555 - 626
15X-RAY DIFFRACTION15chain 'B' and (resid 627 through 659 )B627 - 659
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 40 )C2 - 40
17X-RAY DIFFRACTION17chain 'C' and (resid 41 through 96 )C41 - 96
18X-RAY DIFFRACTION18chain 'C' and (resid 97 through 157 )C97 - 157
19X-RAY DIFFRACTION19chain 'C' and (resid 158 through 273 )C158 - 273
20X-RAY DIFFRACTION20chain 'C' and (resid 274 through 314 )C274 - 314
21X-RAY DIFFRACTION21chain 'C' and (resid 315 through 505 )C315 - 505
22X-RAY DIFFRACTION22chain 'C' and (resid 506 through 554 )C506 - 554
23X-RAY DIFFRACTION23chain 'C' and (resid 555 through 659 )C555 - 659
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 96 )D1 - 96
25X-RAY DIFFRACTION25chain 'D' and (resid 97 through 254 )D97 - 254
26X-RAY DIFFRACTION26chain 'D' and (resid 255 through 293 )D255 - 293
27X-RAY DIFFRACTION27chain 'D' and (resid 294 through 505 )D294 - 505
28X-RAY DIFFRACTION28chain 'D' and (resid 506 through 554 )D506 - 554
29X-RAY DIFFRACTION29chain 'D' and (resid 555 through 659 )D555 - 659

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