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Basic information

Entry
Database: PDB / ID: 5dm3
TitleCrystal Structure of Glutamine Synthetase from Chromohalobacter salexigens DSM 3043(Csal_0679, TARGET EFI-550015) with bound ADP
ComponentsL-glutamine synthetase
KeywordsLIGASE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / nucleotide binding
Similarity search - Function
Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / L-glutamine synthetase
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal Structure of Glutamine Synthetase from Chromohalobacter salexigens DSM 3043(Csal_0679, TARGET EFI-550015) with bound ADP
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionSep 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-glutamine synthetase
B: L-glutamine synthetase
C: L-glutamine synthetase
D: L-glutamine synthetase
E: L-glutamine synthetase
F: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,55712
Polymers319,9946
Non-polymers2,5636
Water1,06359
1
A: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7602
Polymers53,3321
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7602
Polymers53,3321
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7602
Polymers53,3321
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7602
Polymers53,3321
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7602
Polymers53,3321
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7602
Polymers53,3321
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
A: L-glutamine synthetase
B: L-glutamine synthetase
C: L-glutamine synthetase
D: L-glutamine synthetase
E: L-glutamine synthetase
F: L-glutamine synthetase
hetero molecules

A: L-glutamine synthetase
B: L-glutamine synthetase
C: L-glutamine synthetase
D: L-glutamine synthetase
E: L-glutamine synthetase
F: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,11524
Polymers639,98912
Non-polymers5,12612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area47790 Å2
ΔGint-98 kcal/mol
Surface area166760 Å2
MethodPISA
8
A: L-glutamine synthetase
hetero molecules

E: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5194
Polymers106,6652
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3810 Å2
ΔGint-20 kcal/mol
Surface area31210 Å2
MethodPISA
9
B: L-glutamine synthetase
hetero molecules

B: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5194
Polymers106,6652
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3630 Å2
ΔGint-18 kcal/mol
Surface area32870 Å2
MethodPISA
10
C: L-glutamine synthetase
hetero molecules

F: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5194
Polymers106,6652
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3680 Å2
ΔGint-24 kcal/mol
Surface area32280 Å2
MethodPISA
11
D: L-glutamine synthetase
hetero molecules

D: L-glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5194
Polymers106,6652
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3520 Å2
ΔGint-25 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.983, 221.339, 199.353
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-613-

HOH

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Components

#1: Protein
L-glutamine synthetase


Mass: 53332.375 Da / Num. of mol.: 6 / Fragment: Glutamine Synthatase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (strain DSM 3043 / ATCC BAA-138 / NCIMB 13768) (bacteria)
Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_0679 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1QZR8, glutamine synthetase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (5mM MgCl2, 5mM ATP, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (.1 M Sodium Citrate:HCl pH 5.6, 10% (w/v) PEG 4000, 10% (v/v) 2-Propanol); Cryoprotection (20% Ethylene glycol, 80% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 13, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→199.35 Å / Num. obs: 90297 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 58.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.068 / Net I/σ(I): 7.1 / Num. measured all: 654205 / Scaling rejects: 214
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.6-2.645.11.7110.82255443870.3070.80998.9
14.24-199.3560.07814.637126230.990.03399

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DIALS0.5.12data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LNI
Resolution: 2.6→74.064 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2741 4511 5 %
Rwork0.2007 85650 -
obs0.2043 90161 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.19 Å2 / Biso mean: 60.585 Å2 / Biso min: 21.65 Å2
Refinement stepCycle: final / Resolution: 2.6→74.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17602 0 162 60 17824
Biso mean--95.11 53.24 -
Num. residues----2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918156
X-RAY DIFFRACTIONf_angle_d1.22924647
X-RAY DIFFRACTIONf_chiral_restr0.0452775
X-RAY DIFFRACTIONf_plane_restr0.0063140
X-RAY DIFFRACTIONf_dihedral_angle_d15.8916447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.62950.41311410.32462764290597
2.6295-2.66050.38381550.31628252980100
2.6605-2.69290.38661640.299228102974100
2.6929-2.7270.38511560.292428112967100
2.727-2.76290.38451620.292728372999100
2.7629-2.80070.35441590.270328222981100
2.8007-2.84080.30421770.247627812958100
2.8408-2.88320.32721860.251228423028100
2.8832-2.92820.33781510.246528172968100
2.9282-2.97620.34181600.237928212981100
2.9762-3.02750.35241480.250828382986100
3.0275-3.08260.34061370.242328673004100
3.0826-3.14190.3261500.239928252975100
3.1419-3.2060.31381380.22828482986100
3.206-3.27570.32821350.218528582993100
3.2757-3.35190.31031330.222228652998100
3.3519-3.43580.27071340.20128492983100
3.4358-3.52870.31171480.201928583006100
3.5287-3.63250.28721450.200128693014100
3.6325-3.74970.25111300.197328612991100
3.7497-3.88370.25891520.192928783030100
3.8837-4.03920.2251920.168128153007100
4.0392-4.2230.2321420.168828783020100
4.223-4.44570.24831460.164228903036100
4.4457-4.72420.21691230.163728752998100
4.7242-5.08880.22871200.165929123032100
5.0888-5.60080.27481580.178429043062100
5.6008-6.41080.26461370.229163053100
6.4108-8.07540.25381660.197929263092100
8.0754-74.09440.23161660.18242988315498
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)
11.4865-0.46470.81932.3907-0.71521.06180.0690.15180.2561-0.5066-0.0631-0.3253-0.20560.4307-0.06420.4996-0.02880.03350.4987-0.04410.405725.6037-43.02036.069
21.1010.0181-1.14411.6266-0.07771.42750.0077-0.0125-0.1408-0.1616-0.1084-0.03020.1930.15820.04120.46130.0110.0040.463-0.01540.365523.544-58.266814.5404
30.9366-0.1196-0.21351.95380.07461.08360.17790.147-0.44670.1221-0.187-0.21680.51660.06460.00290.54960.0984-0.03810.4886-0.05030.571633.4396-71.646120.9532
42.0671-0.5108-2.86810.40011.50095.22040.0941-0.0632-0.2804-0.1796-0.19020.1476-0.64850.21940.19790.35270.11-0.00860.5722-0.0110.542640.8294-56.598132.8725
52.10150.92090.19181.64180.05571.5704-0.08060.20930.204-0.24650.26030.139-0.1452-0.1549-0.13930.43770.05630.03190.440.11520.4175-20.4279-3.263217.3363
61.15791.62920.55484.1-0.25280.79740.1820.07290.3481-0.6386-0.0921-0.013-0.4388-0.2870.02310.63570.04810.15110.39450.08880.5643-15.452913.010920.9686
72.3548-0.07660.01681.79471.01361.88950.1653-0.05070.03840.052-0.1323-0.09610.15260.4128-0.07950.5075-0.00420.09350.37880.04090.34512.9828-4.846521.046
80.7031-0.52820.27231.8655-0.04962.13730.0393-0.11740.12680.02780.0881-0.0137-0.40720.1081-0.12440.5211-0.01040.11060.4015-0.0090.44762.31578.615225.1999
91.43630.0914-0.18055.4199-2.51086.05950.1077-0.29980.03830.5674-0.5214-0.9945-0.4210.68380.33050.6064-0.20390.00760.7748-0.12060.613313.93913.958830.157
100.61820.3310.34310.4712-0.66281.76780.1183-0.06060.06120.0986-0.1129-0.1476-0.6230.3787-0.01030.7278-0.1220.07630.4904-0.02570.55414.455117.649324.9067
111.5859-1.2560.44233.5079-2.28463.3097-0.2374-0.30360.2955-0.1650.4292-0.0838-0.4292-0.7365-0.05430.62070.03640.09150.4321-0.10030.4926-6.461312.139343.6778
123.2373-0.44550.17731.4746-0.7721.183-0.05420.12230.18230.010.046-0.0743-0.2254-0.12510.02340.45090.01010.03570.36120.03580.353516.6858-6.765411.2564
131.61770.29430.51151.86820.40761.8875-0.04350.06650.0298-0.15050.0379-0.11090.268-0.19180.00770.36210.00310.03190.4352-0.02180.3526.1041-23.940516.3615
141.53370.21530.34061.3202-0.31241.80830.05110.2541-0.16-0.06090.025-0.32070.2740.4428-0.08010.41510.0642-0.03890.5835-0.0390.526244.0175-20.712219.1756
151.54360.223-1.35391.6913-1.62352.66880.07790.01350.37280.34060.16260.1043-0.5753-0.1503-0.0520.5318-0.2024-0.05340.53-0.11230.511236.0429-8.699734.2063
161.98071.1973-0.88962.5517-0.00981.8882-0.22810.15070.1281-0.26880.1508-0.09380.19430.24230.04680.44620.0214-0.01770.4642-0.05540.39544.0827-71.304112.4642
171.59170.33660.14611.1478-0.26011.3520.0077-0.0339-0.0797-0.0236-0.00910.13680.1787-0.1983-0.01070.37380.0034-0.08210.3337-0.01680.3424-11.579-77.013524.1456
180.46570.49490.61391.5051.37632.57570.0514-0.2017-0.18780.36110.0565-0.05250.4308-0.0914-0.10510.52450.0079-0.08610.38130.06420.4807-9.1089-88.941536.0772
193.3403-0.8123-1.14761.6604-0.83981.56520.02920.2909-0.2461-0.2349-0.0740.13210.2385-0.2260.04220.4004-0.0461-0.12630.4161-0.02490.4233-32.2242-66.227421.8338
201.6170.1020.6561.7521-0.00982.16340.10860.0041-0.00590.0942-0.09840.3614-0.2023-0.2382-0.00430.2895-0.015-0.08320.42030.01180.4521-40.8422-49.618230.5132
212.01970.35510.28671.5987-0.98092.05570.22970.4052-0.11930.072-0.02920.1206-0.0416-0.2908-0.15550.41550.0677-0.02360.4827-0.02020.4578-42.6238-50.508133.8754
221.6592-0.5897-0.08080.3036-0.03041.55520.0899-0.0303-0.02230.0960.11630.3204-0.1772-0.4546-0.17390.3437-0.00840.05590.55440.12290.6204-54.5349-53.482243.0688
233.15542.98222.99873.59042.49263.44160.15550.1879-0.43890.5950.42580.25760.493-0.2209-0.39230.565-0.06720.02910.53550.18310.5486-40.1126-65.163252.3784
241.44560.059-0.70363.42121.15351.2985-0.03910.11820.0185-0.2296-0.09620.3252-0.0445-0.32470.10960.36280.0428-0.09880.4890.09390.467-42.8084-31.290423.2684
250.95520.5848-0.32891.70590.11861.71210.01850.12130.1973-0.1830.03470.0523-0.114-0.0422-0.05590.40950.0812-0.01680.41740.09370.4501-34.7889-15.763430.7211
261.40980.15590.14531.72780.32931.56-0.05520.18090.34610.24940.02910.0663-0.5964-0.1068-0.03610.47010.11510.06290.42550.14030.5706-44.8495-0.128837.1531
272.77640.06860.72580.7471-0.45561.44850.1795-0.21290.0875-0.08040.13150.2721-0.0373-0.4257-0.23080.45180.09850.08890.50020.04860.4621-45.5123-16.755852.3019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 99 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 242 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 409 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 410 through 451 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 99 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 134 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 135 through 220 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 221 through 315 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 316 through 340 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 341 through 400 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 401 through 451 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 119 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 120 through 242 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 243 through 409 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 410 through 451 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 4 through 99 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 100 through 285 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 286 through 451 )D0
19X-RAY DIFFRACTION19chain 'E' and (resid 4 through 119 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 120 through 220 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 221 through 285 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 286 through 400 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 401 through 451 )E0
24X-RAY DIFFRACTION24chain 'F' and (resid 5 through 99 )F0
25X-RAY DIFFRACTION25chain 'F' and (resid 100 through 260 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 261 through 400 )F0
27X-RAY DIFFRACTION27chain 'F' and (resid 401 through 450 )F0

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