[English] 日本語
Yorodumi
- PDB-5dm3: Crystal Structure of Glutamine Synthetase from Chromohalobacter s... -

+
Open data


ID or keywords:

Loading...

-
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 (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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