[English] 日本語
Yorodumi
- PDB-4ozd: Crystal structure of PdSP15a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ozd
TitleCrystal structure of PdSP15a
Components14.4 kDa salivary protein
KeywordsPROTEIN BINDING / Salivary / sandfly / vaccine / Leishmania
Function / homologyPheromone/general odorant binding protein domain / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / 14.4 kDa salivary protein
Function and homology information
Biological speciesPhlebotomus duboscqi (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAndersen, J.F. / Alvarenga, P.H.
CitationJournal: To be published
Title: Protection against cutaneous leishmaniasis in non-human primates by immunization with an insect salivary protein
Authors: Oliveira, F. / Rowton, E. / Gomes, R. / Castrovinci, P.A. / Lawyer, P.G. / Teixeira, C. / Aslan, H. / Kleeman, L. / Meneses, C. / Rowland, T. / Gilmore, D. / Andersen, J. / Alvarenga, P.H. / ...Authors: Oliveira, F. / Rowton, E. / Gomes, R. / Castrovinci, P.A. / Lawyer, P.G. / Teixeira, C. / Aslan, H. / Kleeman, L. / Meneses, C. / Rowland, T. / Gilmore, D. / Andersen, J. / Alvarenga, P.H. / Kamhawi, S. / Valenzuela, J.G.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Mar 21, 2018Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen
Item: _diffrn_detector.pdbx_collection_date / _entity_src_gen.pdbx_host_org_scientific_name ..._diffrn_detector.pdbx_collection_date / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14.4 kDa salivary protein
B: 14.4 kDa salivary protein
C: 14.4 kDa salivary protein
D: 14.4 kDa salivary protein
E: 14.4 kDa salivary protein
F: 14.4 kDa salivary protein
G: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)101,2747
Polymers101,2747
Non-polymers00
Water27015
1
A: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.558, 79.730, 232.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
14.4 kDa salivary protein


Mass: 14467.659 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebotomus duboscqi (insect) / Gene: M02 / Organ: Salivary Gland / Plasmid: pET-17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q06KA5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10 % PEG 6000, 0.1M MES pH 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 24313 / % possible obs: 97.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 77.93 Å2 / Rmerge(I) obs: 0.106 / Χ2: 1.738 / Net I/av σ(I): 16.276 / Net I/σ(I): 12.8 / Num. measured all: 128620
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.95-35.50.74911821.50599.7
3-3.065.70.68812481.57799.5
3.06-3.115.70.59911751.54399.7
3.11-3.185.70.47212041.60399
3.18-3.255.60.41712431.74299.2
3.25-3.325.70.33311921.92998.7
3.32-3.415.60.27111982.0398.5
3.41-3.55.60.24612052.15698.4
3.5-3.65.60.18612352.2198.5
3.6-3.725.50.15611852.30297.8
3.72-3.855.40.1412131.90998.1
3.85-45.40.11711981.98397.7
4-4.195.20.09212331.81897.9
4.19-4.415.10.08212071.6398.1
4.41-4.685.10.07512081.55897.3
4.68-5.0450.07112331.52297.2
5.04-5.554.90.07712071.64896.8
5.55-6.354.80.07612151.47295.9
6.35-84.50.06712431.30395.5
8-504.20.0612890.96292.4

-
Processing

Software
NameVersionClassification
HKL-3000phasing
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→40.141 Å / FOM work R set: 0.7617 / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1210 4.99 %Random selection
Rwork0.1999 23041 --
obs0.2031 24251 97.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.03 Å2 / Biso mean: 88.01 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.95→40.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6993 0 0 15 7008
Biso mean----99999 -
Num. residues----840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067138
X-RAY DIFFRACTIONf_angle_d1.0939510
X-RAY DIFFRACTIONf_chiral_restr0.0411007
X-RAY DIFFRACTIONf_plane_restr0.0051183
X-RAY DIFFRACTIONf_dihedral_angle_d15.3392771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.06530.32971100.25632444255494
3.0653-3.20470.30541370.25622569270699
3.2047-3.37360.3461390.24392543268299
3.3736-3.58480.30031420.21792554269699
3.5848-3.86140.27511240.19972588271298
3.8614-4.24960.24381220.17922550267298
4.2496-4.86370.23881290.16332594272398
4.8637-6.12420.25631540.19792595274997
6.1242-40.14490.23861530.22604275793
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.34551.8802-5.28141.4928-1.89965.27020.092-0.0883-0.6939-0.15660.7077-0.28480.56930.8704-1.12240.69820.1072-0.08040.699-0.08340.6239-1.88115.2111-45.8694
22.0037-4.734-8.40932.06293.65558.2235-3.3322-0.9390.0771-0.72480.31923.16322.21370.01081.13071.165-0.1956-0.07020.49330.08491.0962-6.4706-5.1639-50.542
35.04020.9411-4.49226.0136-0.27634.06010.086-0.0689-0.5687-0.0398-0.03060.0023-0.25780.3816-0.09390.34830.0082-0.03790.3366-0.06060.4379-14.63666.6572-47.4968
48.51272.1991-1.91295.00962.08832.47960.7070.77281.90481.5610.4022.0798-0.45210.1893-1.28840.72810.08710.29170.64230.00211.0425-18.013820.0637-47.9411
55.77931.9469-0.46768.5148-2.15745.4758-0.19160.84330.7341-0.86340.48310.4007-0.6429-0.7943-0.36560.6920.11960.14530.5807-0.04190.4946-24.715613.4428-54.3368
67.78215.9814-4.84185.4988-4.01083.8226-0.02330.22950.38640.43540.71781.43570.6704-1.0531-0.47880.52040.13760.05830.4012-0.07570.4801-18.58267.68-57.4728
79.4903-3.18086.18834.3084-3.36255.26080.53660.6107-0.2518-0.09110.1509-0.3997-0.52121.0131-0.31450.7303-0.0120.04930.4733-0.13430.4777-7.902317.6793-54.4674
82.04570.37650.44872.2596-0.09427.9481-0.20380.0059-0.1008-1.05140.00181.0288-0.32931.28140.1620.530.019-0.0720.8951-0.09440.62824.399230.0677-35.9819
96.179-3.53050.5914.3841-0.54738.3690.2988-0.4148-0.5141-0.11460.20620.47510.2685-0.6544-0.36580.3729-0.082-0.06950.46910.08730.44854.754528.3727-31.0598
107.0307-2.0483-5.54958.25922.5237.7863-0.4329-0.4532-0.64790.06040.44070.18441.31790.93270.11620.8016-0.0878-0.13010.4884-0.01910.524712.760217.6282-28.4926
110.5039-1.3199-1.00587.9162-1.5215.67420.7152-0.59040.3653-0.2429-0.37590.24881.30130.1757-0.04020.8514-0.08050.01490.45830.01180.599910.188627.7545-52.1726
124.95220.4590.62169.0248-4.4095.27610.20590.70220.2168-0.8498-0.01360.20590.94650.7315-0.18560.5040.0230.03770.5367-0.10750.41337.23539.584-52.0736
131.60111.05082.25537.5515-1.72834.71560.67540.9091.0565-0.78080.4572.2763-0.0523-1.5002-0.8490.62410.33930.03760.84170.09850.8396-6.867644.4581-50.3807
142.14552.6012-2.42255.9325-0.49065.9497-0.2043-0.38780.57250.93310.3410.9364-1.0779-0.3174-0.030.62210.16650.09080.5630.01060.71931.494453.0219-44.5403
154.03633.7864-2.17545.5225-4.09885.24390.4056-0.9424-0.16280.7822-0.2759-0.0565-0.98220.2315-0.15560.62830.0719-0.01530.4573-0.090.36037.603945.4906-42.7619
166.73070.0817-2.19454.35593.3013.7233-0.117-0.0633-0.4540.4963-0.3053-0.12852.1417-1.24220.24290.9923-0.10610.07370.67030.14470.5312-4.98632.9719-47.6065
174.7485-4.2916-3.98264.68141.23939.87980.33640.7833-0.1828-0.46860.18140.0643-1.3488-0.1018-0.27561.0547-0.1354-0.12930.6767-0.17670.7208-18.368913.8646-29.6293
184.18791.5987-1.02137.2265-0.64936.60940.23880.58840.46350.1056-0.22810.07590.37710.73290.27970.4352-0.0753-0.0670.7106-0.10150.4931-17.51295.5372-32.7781
198.4975-3.89481.71554.8806-4.19194.0887-0.5963-1.20430.21461.16550.74020.9413-0.3083-1.2464-0.4220.6695-0.0580.1530.6464-0.14990.658-33.3721.1088-30.933
206.3775-5.6361-0.89517.07940.73445.560.62042.0473-0.1839-0.6626-0.64921.03711.3149-1.20140.18230.8974-0.26230.07270.7922-0.02580.7008-33.7782-8.3851-37.6365
214.9657-4.11224.09176.4627-7.64679.3307-0.46390.44480.8834-2.27790.2483-2.43680.781.67270.00321.2108-0.2310.27820.5914-0.15330.643-17.5283-11.9635-33.871
224.9351-5.4794.86096.1284-5.49064.9321.1527-0.07830.8776-0.719-0.2897-0.18780.9280.3517-0.35360.5551-0.18840.14460.6149-0.03710.5263-24.8181-2.3224-40.4044
236.87142.42981.43217.91773.32896.82330.07980.24990.7475-0.8340.21390.3447-0.8051-0.5049-0.39880.78830.01350.11680.6865-0.08160.6093-32.217810.501-37.6903
247.38053.27184.28797.0503-0.26073.4279-1.18161.45890.1638-1.61961.3364-0.7869-1.68591.08740.12421.1492-0.35090.0750.9581-0.03330.9373-36.089445.0837-19.8362
253.45172.16152.17572.82673.78845.8587-0.06410.68310.14070.10.6644-0.3381-0.54920.4512-0.46810.5025-0.11590.02870.5448-0.02870.3805-39.729133.3186-19.2491
264.9874.14185.49265.14932.34089.30510.06791.2685-1.2646-1.37660.9922-0.87660.28981.5284-1.491.00340.3189-0.09751.1994-0.33240.8361-29.384922.3459-17.0596
273.71181.13040.67163.24370.12716.43840.1245-1.1299-0.52440.90830.6014-0.2920.8957-0.2268-0.86350.7899-0.048-0.10350.5323-0.10420.5932-42.911723.761-11.0717
287.00490.49182.04425.35381.88775.68140.3659-1.31460.06070.31170.2668-1.3620.34034.4418-0.90511.2354-0.0572-0.00231.3706-0.50590.905-27.539529.0826-8.5079
296.25327.721-1.79342.0068-1.3211.0239-0.3030.04540.3926-0.6201-2.8265-0.6598-0.46292.9791.38141.3744-0.16760.14122.0522-0.27610.9983-26.076336.2314-23.9387
305.3359-0.0045-0.41286.49492.79076.3934-0.35510.0728-0.1066-0.2241-0.33970.3763-0.7787-0.94040.45310.9430.00270.12890.7489-0.07670.5375-24.6191-0.5115-14.6589
316.4883-0.22392.9061.40031.14033.10750.285-0.1087-1.2020.17080.2191-0.05311.6131-0.3709-0.36051.5349-0.11650.01810.56570.0810.7885-16.4795-18.457-16.6283
329.38641.7931-0.11233.18130.22684.98460.09580.23280.0716-0.07850.03670.46981.5185-0.47390.10130.9902-0.1429-0.01290.49310.1140.4945-21.3395-11.469-20.7019
339.5139-1.7023-2.55371.73083.11355.5231-0.7573-0.38810.2196-0.1950.70450.85141.0783-1.1835-0.96411.34-0.37350.27260.7714-0.05131.1065-18.7843-12.80065.2516
342.0606-1.5270.63693.76553.65436.68050.2229-0.74610.5396-1.5271-0.22090.45510.3872-0.93440.28541.1333-0.874-0.23241.2694-0.23860.4649-25.0369-3.89310.1547
354.23272.26560.64374.46250.83883.56750.5707-0.81120.35580.2488-0.36490.4801-0.0686-0.2673-0.22770.83610.15650.1130.6080.00750.4638-9.1014-4.15413.0987
364.720.3454-0.34776.93444.00548.58110.35850.3861-1.64790.39811.5908-2.12761.6721.5646-1.9111.22990.3703-0.20761.0386-0.27750.9864.0411-11.68571.6175
376.2883-0.7172-1.13661.6857-1.73216.40311.08120.77250.3763-0.7305-0.3682-0.8167-0.1182.0994-0.38670.91580.11960.08370.9316-0.13390.64365.0753-0.3501-4.404
387.8151-4.4095-2.89134.43115.297.50520.62570.6536-0.5628-2.1408-0.68510.8452-1.1768-0.2881-0.23810.74040.068-0.02730.6569-0.15290.5297-4.7172-0.4949-6.3312
398.93085.5092-6.33347.6206-4.93634.679-0.69790.4422-0.8302-0.19620.1549-0.53030.1535-0.82840.67741.291-0.0144-0.23410.68020.0930.6773-5.9471-17.8878-0.8316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 17 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 39 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 52 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 87 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 88 through 100 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 122 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 17 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 100 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 122 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 17 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 39 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 40 through 57 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 58 through 81 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 82 through 105 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 106 through 122 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 10 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 11 through 29 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 30 through 57 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 58 through 81 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 82 through 87 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 88 through 100 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 101 through 122 )D0
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 17 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 18 through 39 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 40 through 57 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 58 through 99 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 100 through 116 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 117 through 122 )E0
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 29 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 30 through 81 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 82 through 122 )F0
33X-RAY DIFFRACTION33chain 'G' and (resid 1 through 10 )G0
34X-RAY DIFFRACTION34chain 'G' and (resid 11 through 17 )G0
35X-RAY DIFFRACTION35chain 'G' and (resid 18 through 39 )G0
36X-RAY DIFFRACTION36chain 'G' and (resid 40 through 57 )G0
37X-RAY DIFFRACTION37chain 'G' and (resid 58 through 81 )G0
38X-RAY DIFFRACTION38chain 'G' and (resid 82 through 105 )G0
39X-RAY DIFFRACTION39chain 'G' and (resid 106 through 122 )G0

+
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