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- PDB-3ii9: Crystal structure of glutaryl-coa dehydrogenase from Burkholderia... -

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Basic information

Entry
Database: PDB / ID: 3ii9
TitleCrystal structure of glutaryl-coa dehydrogenase from Burkholderia pseudomallei at 1.73 Angstrom
ComponentsGlutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SlipChip / Microfluidics / Screening / Optimization / protein crystallization / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / FAD / Flavoprotein / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase (ETF) / glutaryl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain ...Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / glutaryl-CoA dehydrogenase (ETF)
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsIsmagilov, R.F. / Li, L. / Du, W.B. / Staker, B. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: User-loaded SlipChip for equipment-free multiplexed nanoliter-scale experiments.
Authors: Li, L. / Du, W. / Ismagilov, R.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Sep 6, 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_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
C: Glutaryl-CoA dehydrogenase
D: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,89122
Polymers173,0254
Non-polymers1,86518
Water16,340907
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20800 Å2
ΔGint-63 kcal/mol
Surface area53040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.966, 141.268, 84.012
Angle α, β, γ (deg.)90.00, 112.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutaryl-CoA dehydrogenase /


Mass: 43256.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1710B / Gene: BURPS1710b_3237 / Plasmid: AVA0421 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21(de3) / References: UniProt: Q3JP94, glutaryl-CoA dehydrogenase

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Non-polymers , 6 types, 925 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 296 K / Method: microfluidic microbatch / pH: 8.5
Details: 19.4% PEG 400, 43 mM Tris 8.5, 86 mM MgCl2, Microfluidic microbatch, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 177485 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 1.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3D6B
Resolution: 1.74→40.23 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.507 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19561 8897 5 %RANDOM
Rwork0.17037 ---
obs0.17164 168491 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.05 Å2
2--0.11 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.74→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11785 0 121 907 12813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212209
X-RAY DIFFRACTIONr_bond_other_d0.0010.028432
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.96616469
X-RAY DIFFRACTIONr_angle_other_deg0.852320453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22451549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20823.25523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.382152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3561598
X-RAY DIFFRACTIONr_chiral_restr0.070.21808
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022513
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2935
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3540.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.57643
X-RAY DIFFRACTIONr_mcbond_other0.1461.53200
X-RAY DIFFRACTIONr_mcangle_it1.192212177
X-RAY DIFFRACTIONr_scbond_it2.01134566
X-RAY DIFFRACTIONr_scangle_it3.3784.54290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.736→1.781 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 595 -
Rwork0.269 11510 -
obs--91.79 %
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)
11.51540.0639-0.65250.6482-0.15280.8181-0.0860.0334-0.3163-0.0971-0.0014-0.06060.16680.05650.08730.11230.01820.0180.0936-0.01520.131938.8743-27.244210.9781
22.38311.0937-0.99391.7103-1.10472.6153-0.1850.3973-0.0308-0.32030.1326-0.06170.0587-0.08670.05240.1593-0.01120.04620.157-0.03850.03749.7521-14.5088-8.9552
31.40750.3198-0.94840.5716-0.4071.7533-0.08150.1601-0.0444-0.1350.0297-0.06820.03360.05520.05190.12620.01250.02380.1165-0.01550.076146.3741-14.64942.0635
40.93190.01030.69070.79560.82225.5806-0.0355-0.076-0.0530.09110.06610.0410.02990.0441-0.03060.09070.01490.00940.10250.01420.104726.876-16.372526.4316
51.74960.40781.62360.81260.36773.9984-0.07230.14790.034-0.07580.01610.0023-0.06060.12470.05620.10110.00180.00120.1356-0.00920.095829.5263-12.27379.4672
69.2569-0.603-6.09611.89624.95915.2715-0.4323-1.7157-0.83470.37070.6122-0.29581.03532.1655-0.17990.51630.1413-0.06970.70290.02750.558742.7335-13.411531.4039
75.6422-0.86581.99089.9117-0.44838.3483-0.04670.21480.1991-0.5284-0.0082-0.1162-0.26140.03480.05480.0715-0.00020.0230.135-0.03440.095441.6581-9.923715.5413
82.9846-0.24820.64126.4228-0.16795.9888-0.09760.27840.2754-0.20790.0824-0.5246-0.38650.39080.01520.1359-0.03080.01170.13380.02680.094328.13790.91280.5803
91.30180.156-0.4940.20590.08860.7663-0.0350.2589-0.0403-0.07460.00620.147-0.0003-0.19210.02880.0763-0.0067-0.04550.15840.0060.1611-0.9615-13.76729.5738
102.1874-0.7075-0.81032.08860.35162.3947-0.1677-0.2458-0.25910.26450.03180.11140.18450.01570.13590.0543-0.00560.03260.10490.030.1691-9.8993-20.24730.7782
111.70670.092-0.77390.6628-0.03030.6987-0.1133-0.1523-0.15330.11260.03790.11450.07550.01230.07540.07250.0047-0.00410.11680.02690.1239-3.7726-15.306128.4512
1227.951122.282-3.297944.6841-0.98728.8253-0.09330.22321.7669-0.10660.2850.1001-0.5277-0.035-0.19160.28410.0588-0.02530.16850.14140.324617.256413.7334-0.0399
131.75192.7842-0.96378.4417-2.68281.4715-0.00240.06880.034-0.1146-0.00270.0702-0.00010.0250.0050.0751-0.0026-0.02250.130.00010.099518.5879-7.67479.2214
140.9352-0.2560.03295.0933-1.24240.9786-0.0652-0.0612-0.04740.13370.10530.0492-0.0346-0.0249-0.040.0713-0.0066-0.00420.10850.01320.121413.628-14.493919.9316
153.03531.9314-1.62062.75630.29662.0336-0.00120.1120.0524-0.0670.00360.0707-0.1-0.0952-0.00240.1530.0047-0.01310.14640.03290.2037.12582.922217.5209
165.0866-0.30841.72265.9649-2.3915.9482-0.0605-0.63980.05850.67490.0530.4739-0.2594-0.72580.00750.190.00130.05110.25050.00470.139416.4792-15.588834.2559
171.0501-0.23630.34440.6134-0.170.6386-0.0248-0.04290.20820.02530.0032-0.1827-0.11880.15120.02160.1108-0.0307-0.02090.1141-0.01220.130352.164614.416733.9361
182.85630.40990.28621.8216-0.2033.2278-0.0005-0.1850.00440.1410.0351-0.1164-0.11060.0111-0.03470.09130.0135-0.05610.1428-0.01410.056753.46313.851951.1406
191.6319-0.161-0.05161.6893-0.67442.5839-0.039-0.2764-0.17680.10380.03170.07180.1094-0.17220.00730.0649-0.0186-0.02730.17480.01660.052851.1195-7.216257.2453
200.6767-0.51920.07720.5843-0.17622.7807-0.0466-0.1703-0.04820.1198-0.0005-0.0070.16560.13280.04720.0938-0.0298-0.02010.1610.00890.099955.574-6.119850.1587
211.4089-0.2850.42690.7413-0.91935.73440.01750.1220.0368-0.07490.0068-0.06260.08440.0914-0.02430.1054-0.018-0.01630.0907-0.00460.108742.33458.738224.5985
220.7927-0.1045-0.22180.63670.2372.6662-0.029-0.06890.07010.04690.0177-0.0116-0.11650.00380.01120.11060.0103-0.02020.096-0.00030.107634.345412.673131.2101
233.7364-1.10671.36423.705-0.40272.75350.01480.30320.0454-0.1752-0.1159-0.109-0.02790.18340.10110.108-0.0042-0.00440.1131-0.00360.075743.70930.861620.5904
244.4791.239-2.42851.3161-0.10963.9868-0.2431-0.1384-0.4440.15360.0571-0.23660.25380.21530.1860.1780.0199-0.01380.11730.03160.117228.4999-1.261942.317
250.7361-0.65520.35031.1439-0.32430.9437-0.1257-0.21830.07630.20670.13410.0095-0.3089-0.2-0.00840.19110.07010.03310.0936-0.00170.078111.538227.392335.3004
263.06981.40230.72072.6321-0.78921.5606-0.01230.01940.08490.12110.10490.1187-0.0912-0.1618-0.09260.15990.05980.02840.0480.02260.130312.842225.118429.8821
271.1542-0.08620.27521.1609-1.38112.6078-0.05230.047-0.00880.09250.10180.0971-0.0965-0.1273-0.04950.15770.0568-0.00350.03640.03140.12848.51435.855811.8258
280.9171-0.18330.4121.482-1.27041.6394-0.04950.11310.0827-0.06210.06610.0367-0.0578-0.0741-0.01660.14880.04830.01190.0470.0170.088610.764831.000511.6066
297.26032.8040.724219.2682-3.85355.31050.1533-0.2332-0.50050.2014-0.010.07940.1844-0.3189-0.14330.10720.01920.02320.12960.05710.108410.8003-0.615142.1065
301.04330.6332-0.35821.5728-0.83991.0579-0.03030.00790.07430.01690.0471-0.0001-0.0753-0.015-0.01680.12710.0235-0.00380.06430.01530.110123.601313.866429.8992
313.0751-0.67351.16197.0278-0.15682.80890.017-0.1331-0.05840.0610.01610.14530.0838-0.1314-0.0330.09930.0143-0.00890.06810.03920.13628.3748.484926.5717
324.22140.3168-3.32635.865-1.60135.2603-0.24810.78670.116-0.69350.13380.478-0.1764-0.66660.11420.2803-0.0042-0.06990.21830.04060.15427.8117.76799.9477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 101
2X-RAY DIFFRACTION2A102 - 196
3X-RAY DIFFRACTION3A197 - 275
4X-RAY DIFFRACTION4A276 - 316
5X-RAY DIFFRACTION5A317 - 346
6X-RAY DIFFRACTION6A347 - 359
7X-RAY DIFFRACTION7A360 - 374
8X-RAY DIFFRACTION8A375 - 395
9X-RAY DIFFRACTION9B4 - 101
10X-RAY DIFFRACTION10B102 - 180
11X-RAY DIFFRACTION11B181 - 276
12X-RAY DIFFRACTION12B277 - 285
13X-RAY DIFFRACTION13B286 - 316
14X-RAY DIFFRACTION14B317 - 345
15X-RAY DIFFRACTION15B346 - 372
16X-RAY DIFFRACTION16B373 - 395
17X-RAY DIFFRACTION17C4 - 98
18X-RAY DIFFRACTION18C99 - 150
19X-RAY DIFFRACTION19C151 - 197
20X-RAY DIFFRACTION20C198 - 243
21X-RAY DIFFRACTION21C244 - 287
22X-RAY DIFFRACTION22C288 - 337
23X-RAY DIFFRACTION23C338 - 369
24X-RAY DIFFRACTION24C370 - 395
25X-RAY DIFFRACTION25D3 - 78
26X-RAY DIFFRACTION26D79 - 100
27X-RAY DIFFRACTION27D101 - 181
28X-RAY DIFFRACTION28D182 - 269
29X-RAY DIFFRACTION29D270 - 284
30X-RAY DIFFRACTION30D285 - 346
31X-RAY DIFFRACTION31D347 - 372
32X-RAY DIFFRACTION32D373 - 395

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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