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- PDB-6q6x: Structure of Fucosylated D-antimicrobial peptide SB6 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6q6x
TitleStructure of Fucosylated D-antimicrobial peptide SB6 in complex with the Fucose-binding lectin PA-IIL at 1.525 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB6
KeywordsANTIBIOTIC / Antimicrobial / Lectin / Complex
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
AMINO GROUP / Chem-ZDC / polypeptide(D) / polypeptide(D) (> 10) / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.525 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Authors: Baeriswyl, S. / Gan, B.H. / Siriwardena, T.N. / Visini, R. / Robadey, M. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionDec 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _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.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.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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
E: SB6
B: Fucose-binding lectin
F: SB6
C: Fucose-binding lectin
G: SB6
D: Fucose-binding lectin
H: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,87624
Polymers52,6668
Non-polymers1,20916
Water9,692538
1
A: Fucose-binding lectin
E: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5097
Polymers13,1672
Non-polymers3425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin
F: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5097
Polymers13,1672
Non-polymers3425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin
G: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4295
Polymers13,1672
Non-polymers2623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fucose-binding lectin
H: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4295
Polymers13,1672
Non-polymers2623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.474, 59.416, 72.060
Angle α, β, γ (deg.)90.000, 106.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Polypeptide(D) / Sugars , 3 types, 12 molecules ABCDEFGH

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose-binding lectin PA-IIL Lectin B from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D)
SB6


Mass: 1431.855 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Fucosylated D-antimicrobial peptide SB6 / Source: (synth.) synthetic construct (others)
#4: Sugar
ChemComp-ZDC / 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid


Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O6

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Non-polymers , 3 types, 550 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NH2 / AMINO GROUP / Amine


Mass: 16.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.525→47.509 Å / Num. all: 62803 / Num. obs: 62803 / % possible obs: 96.8 % / Redundancy: 2.8 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.081 / Rsym value: 0.066 / Net I/av σ(I): 10.3 / Net I/σ(I): 13.9 / Num. measured all: 175314
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.53-1.612.60.4351.72095281320.3170.5410.4353.286.4
1.61-1.712.70.3472.22375187670.2430.4250.3474.498.2
1.71-1.822.90.233.12405683460.1550.2780.236.799.3
1.82-1.972.90.1345.32214977550.090.1620.13410.399.3
1.97-2.162.70.0848.51940970820.060.1040.08413.898.1
2.16-2.412.70.06121763064140.0430.0740.0617.798.2
2.41-2.7830.0514.51701956870.0330.060.0521.399
2.78-3.412.90.03619.81400148140.0240.0430.0362798.6
3.41-4.822.70.02525.3995837350.0180.0310.02534.597.7
4.82-47.5093.10.02621.9638920710.0180.0320.02638.197

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.83 Å47.51 Å
Translation3.83 Å47.51 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.525→47.509 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 5572 5 %
Rwork0.1582 105795 -
obs0.1594 62774 87.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.94 Å2 / Biso mean: 15.3213 Å2 / Biso min: 5.86 Å2
Refinement stepCycle: final / Resolution: 1.525→47.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 64 538 4275
Biso mean--10.74 29.41 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063773
X-RAY DIFFRACTIONf_angle_d0.8465152
X-RAY DIFFRACTIONf_chiral_restr0.069652
X-RAY DIFFRACTIONf_plane_restr0.004671
X-RAY DIFFRACTIONf_dihedral_angle_d5.3092098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5251-1.54240.331150.28632108222353
1.5424-1.56060.37381710.27343361353282
1.5606-1.57960.25241660.26633179334581
1.5796-1.59960.27381770.25553238341580
1.5996-1.62060.28811840.25833390357484
1.6206-1.64280.23861810.25043419360084
1.6428-1.66630.29321720.22543419359186
1.6663-1.69120.23811930.20753560375388
1.6912-1.71760.24571810.18993591377289
1.7176-1.74580.21281930.17543593378689
1.7458-1.77590.16111800.1663582376289
1.7759-1.80820.22931980.16553652385090
1.8082-1.84290.19321890.15973581377090
1.8429-1.88060.16381910.15033659385090
1.8806-1.92150.1941860.14873589377590
1.9215-1.96610.16991860.13833664385090
1.9661-2.01530.15722060.12843630383690
2.0153-2.06980.16481890.13813573376289
2.0698-2.13070.13911930.13563587378088
2.1307-2.19950.1861800.13543494367486
2.1995-2.27810.17561970.13333572376988
2.2781-2.36930.15141810.13373579376090
2.3693-2.47710.20222000.13893773397393
2.4771-2.60770.17911930.14883719391293
2.6077-2.77110.19941970.14563766396392
2.7711-2.9850.18451860.1483652383892
2.985-3.28530.17541980.14633720391892
3.2853-3.76060.11681920.12853685387791
3.7606-4.73720.16281920.14343615380790
4.7372-47.5320.15812050.18943845405095
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)
10.488-0.1438-0.07210.2946-0.10230.39640.00450.00270.05750.0021-0.0040.0334-0.0427-0.0024-0.010.07520.0020.0040.08550.00410.0712-16.675-4.0335-19.1102
21.26420.9349-1.73620.9318-1.41973.45350.0795-0.0850.16660.1001-0.04260.0693-0.32060.0515-0.08420.1151-0.0050.00430.09270.00210.1089-12.86632.789-18.7836
35.5484-2.44580.65473.55671.91512.0358-0.0656-0.27090.16110.3511-0.12310.63140.0476-0.16690.00260.1121-0.00970.00860.1412-0.03370.2005-20.33350.1531-4.7642
40.31930.01690.06850.1711-0.0460.01180.0024-0.00950.0151-0.00260.0134-0.00050.01620.0121-0.00150.07380.0090.0040.0838-0.00160.0651-8.4757-8.5776-16.5677
50.67670.32980.19211.88560.46990.4866-0.0260.150.0428-0.1993-0.01970.0331-0.1202-0.0847-0.00430.09460.0062-0.01260.11160.01420.111-42.9647-6.4128-28.7948
60.8557-0.70440.35531.2696-0.64190.9076-0.13410.04040.03740.22140.0956-0.2197-0.10.0580.01190.0696-0.0081-0.00430.0843-0.0020.0992-32.7335-13.1352-18.1213
70.57870.3523-0.16880.5806-0.17830.87720.00610.3165-0.0188-0.1371-0.12010.0317-0.0180.07570.03110.1106-0.0004-0.00640.14860.00240.1124-32.1026-11.4113-28.8756
82.1223-1.16581.57713.283-1.92171.7863-0.00440.2557-0.0215-0.103-0.0355-0.15090.06230.0590.05120.07060.01290.00430.14410.01110.1243-27.8517-10.477-26.4522
90.8113-0.23770.27031.0546-0.17490.64670.00360.0411-0.01880.14190.0358-0.0165-0.0414-0.01850.02830.07950.00870.00580.0749-0.00370.1105-30.0864-12.1671-16.1947
100.6494-0.72560.45952.5746-0.72590.98230.15330.28930.0003-0.4245-0.2269-0.06360.03350.02140.02950.13770.03210.01050.13610.02640.1016-36.985-8.4453-30.31
113.4117-0.0158-1.29231.50640.63312.42850.05580.1864-0.1289-0.01940.1221-0.24990.26760.3495-0.02030.13490.0327-0.0150.2035-0.06620.1412-30.0153-24.3222-27.9175
120.848-0.5547-0.17430.74530.30050.2620.04050.07540.02820.0731-0.0534-0.0990.0222-0.0305-0.00580.07090.0065-0.00250.0825-0.00370.0927-45.4696-10.265-20.0084
130.42430.0289-0.01590.472-0.07330.34940.06220.0235-0.045-0.0192-0.07560.04220.0192-0.02220.00110.07950.0025-0.00650.076-0.00780.1073-38.7934-16.2128-18.8942
140.62250.3563-0.33520.5356-0.3850.9223-0.1344-0.0297-0.0560.10520.1244-0.11820.1320.02840.02180.1230.0126-0.00750.09650.01410.1009-3.9043-26.6134-15.8388
150.1983-0.04020.24480.6647-0.6521.67010.01260.0018-0.0557-0.03920.0610.04550.1130.00390.00580.0918-0.0072-0.00470.0881-0.00030.0776-12.812-23.9933-25.4871
162.2372-0.71220.85320.6157-0.55662.79920.0721-0.0896-0.3085-0.04190.06950.11190.20530.0039-0.08860.1258-0.0185-0.01210.11070.00280.0788-15.8063-29.6177-25.2971
170.53070.0507-0.11590.18670.01440.88720.01140.03160.002-0.04560.05150.06060.0842-0.0118-0.01960.0851-0.0073-0.00780.09890.00060.0726-17.623-18.968-26.425
180.1298-0.18570.30610.5169-1.17432.6435-0.02630.0248-0.0464-0.0926-0.02590.0260.34930.12920.00850.13650.00950.00380.0890.01490.0852-7.6192-29.5139-21.435
190.46760.16750.34830.25640.3160.42230.00640.0478-0.01370.00020.0408-0.03170.05340.0165-0.00320.0760.00250.00040.0792-0.0010.075-4.3626-17.9724-25.7868
200.16950.0289-0.08880.0709-0.14060.49170.0417-0.0423-0.05430.0003-0.0537-0.0042-0.12-0.0410.00070.0973-0.0096-0.00910.07850.00620.054-11.3635-18.7525-16.3394
210.9966-0.3330.05721.2976-0.02430.5817-0.0665-0.0299-0.11450.1041-0.00760.09710.0384-0.1415-0.01060.0825-0.00490.00140.09780.01750.1106-48.964-15.6765-2.4471
220.41620.24180.08591.561-0.41460.6024-0.0089-0.1162-0.02910.0833-0.079-0.114-0.05460.026-0.01580.0863-0.00160.00140.0967-0.00440.1025-38.9298-6.8849-2.6326
230.821.2543-1.18632.6375-2.40362.6015-0.0484-0.12240.14070.08550.0312-0.1428-0.0966-0.1727-0.00720.12010.0048-0.00510.12450.00080.1147-36.2603-7.35892.5352
241.32010.22910.9783.50631.55713.1543-0.00370.07940.1409-0.16480.0345-0.1259-0.12880.2052-0.00510.1032-0.0095-0.00190.10520.00240.1273-32.84443.5693-11.4196
250.51181.421-0.57244.6898-1.96790.85020.0349-0.0145-0.1250.1439-0.0557-0.29120.02430.00820.06810.1112-0.00440.00160.10630.00990.136-33.9145-11.6032-4.2034
260.42160.22220.00681.38120.10380.25470.0667-0.1569-0.02590.2846-0.08090.1095-0.0487-0.03030.00090.11980.00090.00270.10770.01580.0977-45.0807-10.91931.6592
271.40861.6310.91032.05811.53511.93670.0173-0.15780.16470.30180.00410.0808-0.3015-0.07120.0250.2063-0.02110.03250.1079-0.00980.1074-43.56745.83681.67
280.29910.24870.180.38650.27950.28570.0242-0.01880.03090.1053-0.0278-0.05090.0321-0.0414-0.00150.08620.00410.00460.0826-0.0140.0903-46.9447-6.2077-10.9806
290.1494-0.10850.06360.5938-0.10380.15920.03380.0048-0.0448-0.08130.0214-0.00440.0240.0787-0.00060.09870.0115-0.00630.0689-0.01070.1018-40.561-15.0009-9.2729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )A1 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 69 )A57 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 74 )A70 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 114 )A75 - 114
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 12 )B1 - 12
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 25 )B13 - 25
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 34 )B26 - 34
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 42 )B35 - 42
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 56 )B43 - 56
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 68 )B57 - 68
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 74 )B69 - 74
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 95 )B75 - 95
13X-RAY DIFFRACTION13chain 'B' and (resid 96 through 114 )B96 - 114
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 12 )C1 - 12
15X-RAY DIFFRACTION15chain 'C' and (resid 13 through 34 )C13 - 34
16X-RAY DIFFRACTION16chain 'C' and (resid 35 through 42 )C35 - 42
17X-RAY DIFFRACTION17chain 'C' and (resid 43 through 56 )C43 - 56
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 69 )C57 - 69
19X-RAY DIFFRACTION19chain 'C' and (resid 70 through 104 )C70 - 104
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 114 )C105 - 114
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 12 )D1 - 12
22X-RAY DIFFRACTION22chain 'D' and (resid 13 through 34 )D13 - 34
23X-RAY DIFFRACTION23chain 'D' and (resid 35 through 42 )D35 - 42
24X-RAY DIFFRACTION24chain 'D' and (resid 43 through 47 )D43 - 47
25X-RAY DIFFRACTION25chain 'D' and (resid 48 through 56 )D48 - 56
26X-RAY DIFFRACTION26chain 'D' and (resid 57 through 69 )D57 - 69
27X-RAY DIFFRACTION27chain 'D' and (resid 70 through 74 )D70 - 74
28X-RAY DIFFRACTION28chain 'D' and (resid 75 through 104 )D75 - 104
29X-RAY DIFFRACTION29chain 'D' and (resid 105 through 114 )D105 - 114

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