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- PDB-3r5b: Pseudomonas aeruginosa DapD (PA3666) in complex with L-2-aminopimelate -

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Basic information

Entry
Database: PDB / ID: 3r5b
TitlePseudomonas aeruginosa DapD (PA3666) in complex with L-2-aminopimelate
ComponentsTetrahydrodipicolinate N-succinyletransferase
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE complex
Function / homology
Function and homology information


2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / magnesium ion binding / cytoplasm
Similarity search - Function
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Trimeric LpxA-like superfamily / 3 Solenoid / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(2S)-2-aminoheptanedioic acid / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.51 Å
AuthorsSandalova, T. / Schnell, R. / Schneider, G.
CitationJournal: Plos One / Year: 2012
Title: Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.
Authors: Schnell, R. / Oehlmann, W. / Sandalova, T. / Braun, Y. / Huck, C. / Maringer, M. / Singh, M. / Schneider, G.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Structure summary
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Tetrahydrodipicolinate N-succinyletransferase
B: Tetrahydrodipicolinate N-succinyletransferase
C: Tetrahydrodipicolinate N-succinyletransferase
D: Tetrahydrodipicolinate N-succinyletransferase
E: Tetrahydrodipicolinate N-succinyletransferase
F: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,60611
Polymers217,7306
Non-polymers8765
Water4,612256
1
A: Tetrahydrodipicolinate N-succinyletransferase
B: Tetrahydrodipicolinate N-succinyletransferase
C: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2165
Polymers108,8653
Non-polymers3502
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-20 kcal/mol
Surface area34880 Å2
MethodPISA
2
D: Tetrahydrodipicolinate N-succinyletransferase
E: Tetrahydrodipicolinate N-succinyletransferase
F: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3916
Polymers108,8653
Non-polymers5263
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-21 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.038, 102.002, 134.903
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12D
22E
32F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 300
2112B1 - 300
3112C1 - 300
1124D1 - 300
2124E1 - 300
3124F1 - 300

NCS ensembles :
ID
1
2

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Components

#1: Protein
Tetrahydrodipicolinate N-succinyletransferase / Tetrahydrodipicolinate succinylase


Mass: 36288.379 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dapD, PA3666 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Z9H2, UniProt: G3XD76*PLUS, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical
ChemComp-NPI / (2S)-2-aminoheptanedioic acid / L-2-AMINOPIMELIC ACID


Type: L-peptide linking / Mass: 175.182 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H13NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 19-20% of PEG3350, 0.3-0.4M succinate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.545
11h,-k,-l20.455
ReflectionResolution: 2.5→37 Å / Num. all: 72498 / Num. obs: 72498 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.51→36.88 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.817 / SU B: 21.379 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27567 3632 5 %RANDOM
Rwork0.25019 ---
obs0.25149 68844 93.94 %-
all-68844 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.868 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20.7 Å2
2--0.72 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.51→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14081 0 60 256 14397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02214363
X-RAY DIFFRACTIONr_bond_other_d0.0030.029446
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.98319481
X-RAY DIFFRACTIONr_angle_other_deg0.9683.00123144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06851895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96524.74538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.075152335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1141570
X-RAY DIFFRACTIONr_chiral_restr0.0840.22319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022698
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_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2541.59419
X-RAY DIFFRACTIONr_mcbond_other0.0511.53942
X-RAY DIFFRACTIONr_mcangle_it0.455214964
X-RAY DIFFRACTIONr_scbond_it0.64834944
X-RAY DIFFRACTIONr_scangle_it1.1034.54517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1695TIGHT POSITIONAL0.020.05
12B1695TIGHT POSITIONAL0.020.05
13C1695TIGHT POSITIONAL0.020.05
11A1833MEDIUM POSITIONAL0.060.5
12B1833MEDIUM POSITIONAL0.050.5
13C1833MEDIUM POSITIONAL0.040.5
11A1695TIGHT THERMAL0.030.5
12B1695TIGHT THERMAL0.030.5
13C1695TIGHT THERMAL0.030.5
11A1833MEDIUM THERMAL0.032
12B1833MEDIUM THERMAL0.032
13C1833MEDIUM THERMAL0.032
21D3521MEDIUM POSITIONAL0.250.5
22E3521MEDIUM POSITIONAL0.230.5
23F3521MEDIUM POSITIONAL0.240.5
21D3521MEDIUM THERMAL0.232
22E3521MEDIUM THERMAL0.222
23F3521MEDIUM THERMAL0.242
LS refinement shellResolution: 2.509→2.574 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 173 -
Rwork0.274 3530 -
obs--64.99 %
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)
11.0503-0.2279-0.20591.3125-0.35160.3047-0.02280.09840.044-0.14630.02940.11070.0158-0.1308-0.00650.1153-0.0019-0.01620.20970.04650.161-21.9547.586-11.926
20.99920.42120.22481.1115-0.29290.5965-0.01090.07950.0796-0.01120.0380.0418-0.0044-0.061-0.02710.1264-0.00840.00890.16580.01950.1348-10.3037.293-10.822
30.565-0.01630.11140.88040.01050.3946-0.0255-0.00190.0222-0.00960.01850.0205-0.0171-0.03680.0070.1034-0.0057-0.00080.16380.02020.119-2.4723.3733.039
41.6450.73020.81852.12510.42512.34690.06250.19130.0248-0.1659-0.0304-0.14180.02170.0789-0.03210.08450.03210.06080.24910.00430.171714.981-7.058-9.299
50.99110.75731.31812.17140.41662.186-0.05030.1504-0.036-0.2275-0.0728-0.41290.0510.08780.12310.11690.03160.13720.2823-0.00280.323628.036-8.226-14.011
63.7405-0.49461.3672.3062-3.28874.86970.53131.8223-0.5382-0.5315-0.20140.14050.93780.5832-0.32980.45050.23020.01670.9081-0.1960.484830.809-13.302-16.656
70.62760.1273-0.06321.09960.10620.8057-0.0305-0.0411-0.10850.05170.02990.05440.118-0.07150.00070.1099-0.01010.0220.1640.00320.1131-12.174-24.14427.268
80.6563-0.12590.0671.04380.23011.1187-0.07460.0141-0.03580.03270.05710.00320.0272-0.04510.01740.1259-0.01470.01850.1609-0.00160.1286-3.178-21.80120.143
90.30920.05010.09520.56540.01260.6483-0.0325-0.0143-0.00590.04190.0294-0.01410.0028-0.02530.00310.1017-0.00410.01710.14590.00790.1130.442-7.13414.105
102.0943-0.5849-0.11521.6908-0.96622.0303-0.00110.0967-0.16840.0108-0.0729-0.15420.02830.03930.07390.07090.00770.01220.20380.02480.184223.724-10.70713.863
111.82041.1634-1.031.5948-0.56731.8734-0.1832-0.1295-0.1459-0.15330.0677-0.32920.15450.27140.11560.04250.05220.03450.22330.00770.302836.431-13.0118.936
122.52372.5295-0.19915.8698-0.09530.02620.2415-0.4809-0.7290.8995-0.3073-0.9197-0.03490.02610.06570.3755-0.0151-0.10590.44460.07370.621940.652-17.82314.33
131.151-0.0139-0.27190.88660.55610.55150.04-0.08550.23450.1654-0.06160.0436-0.0664-0.05070.02150.24240.01120.01780.1808-0.02360.1718-2.6426.31631.864
141.1131-0.20320.21790.9112-0.16111.1699-0.0323-0.09670.08510.1267-0.01560.0445-0.0326-0.00810.04780.1771-0.005-0.00590.1547-0.00630.15665.82319.76827.008
150.50510.0563-0.0890.6407-0.23990.7412-0.0058-0.00280.02930.04450.00320.0131-0.0095-0.00430.00260.10670.01680.00320.15090.00020.12393.3687.72216.254
161.0952-0.04920.24242.66110.560.52930.03630.00760.11540.0891-0.0564-0.197-0.01230.08910.02020.1116-0.03010.02950.21990.03480.18523.49312.6134.913
170.7880.6629-0.20072.35020.50110.92180.06770.11190.02060.17890.1045-0.53350.05820.0245-0.17220.04750.00550.0330.2160.0620.340236.1599.260.115
182.6497-1.3291-1.39380.67480.71360.95840.40990.02910.7693-0.1969-0.0391-0.3574-0.05810.117-0.37080.20690.02230.14150.47030.02570.64240.72516.977-0.893
191.04430.31440.30081.04-0.31780.5985-0.0285-0.1199-0.05030.14370.03960.08810.0084-0.123-0.01110.09930.0040.03330.18730.04140.159219.246-18.62478.728
200.8673-0.5928-0.32221.4661-0.35060.47640.01060.0005-0.06440.05220.03970.0498-0.0014-0.0295-0.05040.12330.01750.01110.17820.02430.145530.904-18.31177.624
210.4357-0.0575-0.20790.7849-0.13120.1785-0.02290.0049-0.0253-0.00910.0198-0.0036-0.0065-0.02180.00310.10040.00760.01050.16330.02040.128838.917-14.19363.983
221.7262-0.2665-0.95740.9882-0.10053.32860.0365-0.1449-0.06330.1107-0.0323-0.1227-0.0530.1404-0.00410.1103-0.0324-0.05190.2491-0.01420.181256.343-4.05476.19
230.4906-0.4164-1.04381.5735-0.13713.1542-0.0447-0.0650.05010.1806-0.0876-0.3353-0.02010.12380.13220.073-0.0414-0.07960.2992-0.01250.302669.142-2.75780.605
241.9545-1.19450.61580.9686-0.65691.7682-0.0179-0.84010.6605-0.05540.0653-0.4102-0.63770.3808-0.04740.53940.0468-0.03641.2137-0.2790.569171.9392.30483.501
250.6764-0.11940.34211.07490.04990.7093-0.02970.02820.109-0.06760.03510.0554-0.1045-0.0659-0.00550.11020.01580.01490.15670.00610.113229.14313.10739.551
260.6472-0.05710.03831.0270.13780.9918-0.03230.0030-0.02710.0474-0.0103-0.0584-0.0808-0.01520.13520.01480.00310.1642-0.00310.12338.10710.76846.679
270.5123-0.0079-0.19780.61730.00110.7292-0.02650.0067-0.0094-0.02670.0274-0.0144-0.0048-0.0101-0.0010.09710.0028-0.00260.14990.00590.11541.741-3.88952.712
281.52040.68460.64411.3204-1.29512.8063-0.0154-0.08660.0983-0.045-0.0587-0.03730.0205-0.0070.07420.06420.00210.03410.2220.01280.210265.004-0.30852.957
295.2109-2.6787-0.10191.4993-0.55953.0825-0.1419-0.02980.30240.1039-0.0361-0.1983-0.1630.30280.17810.0268-0.0653-0.01780.21090.00290.318177.6951.92657.916
300.15790.91720.04025.65220.20210.0222-0.11520.0314-0.0682-0.92870.0993-0.2120.0250.00270.01590.38690.00630.07230.4660.01450.490682.0786.66552.434
311.0885-0.01490.37690.95760.50180.49160.05260.1076-0.2018-0.1624-0.05930.05230.0581-0.04780.00660.2458-0.01740.00620.1802-0.01610.168838.744-37.31534.949
320.70360.3014-0.31290.8771-0.1110.8344-0.01350.1204-0.1083-0.1410.01120.04620.0426-0.04540.00220.17570.00420.01660.1676-0.00150.163647.194-30.76539.804
330.419-0.07210.17910.5183-0.26330.6966-0.01030.0057-0.0058-0.0509-0.00930.01290.0192-0.01760.01970.1088-0.01010.01110.1613-0.00080.136544.694-18.7350.549
340.5332-0.7455-0.81722.50040.89871.45890.0265-0.0335-0.0227-0.13160.0053-0.17670.07550.1583-0.03170.11050.0252-0.01180.22040.01510.204864.775-23.61861.928
351.30790.61281.26440.65440.75581.78380.0901-0.1265-0.1181-0.08540.0391-0.4108-0.06780.1261-0.12920.0923-0.02730.10770.26870.0310.418177.413-20.23966.801
363.16970.5649-1.46810.2085-0.66262.5196-0.0959-0.0112-0.75590.0676-0.0124-0.0849-0.2027-0.38060.10840.1307-0.108-0.11270.50810.13530.757682.295-27.74267.738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 80
2X-RAY DIFFRACTION2A81 - 132
3X-RAY DIFFRACTION3A133 - 229
4X-RAY DIFFRACTION4A230 - 280
5X-RAY DIFFRACTION5A281 - 320
6X-RAY DIFFRACTION6A321 - 329
7X-RAY DIFFRACTION7B3 - 80
8X-RAY DIFFRACTION8B81 - 132
9X-RAY DIFFRACTION9B133 - 232
10X-RAY DIFFRACTION10B233 - 282
11X-RAY DIFFRACTION11B283 - 322
12X-RAY DIFFRACTION12B323 - 328
13X-RAY DIFFRACTION13C3 - 80
14X-RAY DIFFRACTION14C81 - 132
15X-RAY DIFFRACTION15C133 - 231
16X-RAY DIFFRACTION16C232 - 279
17X-RAY DIFFRACTION17C280 - 322
18X-RAY DIFFRACTION18C323 - 329
19X-RAY DIFFRACTION19D3 - 80
20X-RAY DIFFRACTION20D81 - 132
21X-RAY DIFFRACTION21D133 - 231
22X-RAY DIFFRACTION22D232 - 279
23X-RAY DIFFRACTION23D280 - 320
24X-RAY DIFFRACTION24D321 - 329
25X-RAY DIFFRACTION25E3 - 80
26X-RAY DIFFRACTION26E81 - 132
27X-RAY DIFFRACTION27E133 - 232
28X-RAY DIFFRACTION28E233 - 282
29X-RAY DIFFRACTION29E283 - 315
30X-RAY DIFFRACTION30E323 - 342
31X-RAY DIFFRACTION31F3 - 80
32X-RAY DIFFRACTION32F81 - 132
33X-RAY DIFFRACTION33F133 - 231
34X-RAY DIFFRACTION34F232 - 279
35X-RAY DIFFRACTION35F280 - 322
36X-RAY DIFFRACTION36F323 - 329

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