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- PDB-2rck: Crystal structure of juvenile hormone binding protein from Galler... -

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Basic information

Entry
Database: PDB / ID: 2rck
TitleCrystal structure of juvenile hormone binding protein from Galleria mellonella hemolymph
ComponentsJuvenile hormone binding protein
KeywordsHORMONE BINDING PROTEIN / Galleria mellonella / hemolymph / JHBP-fold / juvenile hormone
Function / homology
Function and homology information


extracellular space
Similarity search - Function
TULIP domain / Haemolymph juvenile hormone binding / Takeout superfamily / Haemolymph juvenile hormone binding protein (JHBP) / Juvenile hormone binding protein domains in insects. / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
Juvenile hormone binding protein
Similarity search - Component
Biological speciesGalleria mellonella (greater wax moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.44 Å
AuthorsKolodziejczyk, R. / Bujacz, G. / Jakob, M. / Ozyhar, A. / Jaskolski, M. / Kochman, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Insect Juvenile Hormone Binding Protein Shows Ancestral Fold Present in Human Lipid-Binding Proteins.
Authors: Kolodziejczyk, R. / Bujacz, G. / Jakob, M. / Ozyhar, A. / Jaskolski, M. / Kochman, M.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE AUTHOR STATES THAT THERE IS A SEQUENCE ERROR IN DATABASE. DATABASE RESIDUE 201 (RESIDUE ...SEQUENCE AUTHOR STATES THAT THERE IS A SEQUENCE ERROR IN DATABASE. DATABASE RESIDUE 201 (RESIDUE 181 IN THE COORDINATES) IS INDEED GLU.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Juvenile hormone binding protein
B: Juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8418
Polymers50,0232
Non-polymers8196
Water1,65792
1
A: Juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4214
Polymers25,0111
Non-polymers4093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4214
Polymers25,0111
Non-polymers4093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.950, 109.950, 94.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Juvenile hormone binding protein


Mass: 25011.379 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GREATER Wax moth / Source: (natural) Galleria mellonella (greater wax moth) / Tissue: hemolymph / References: UniProt: Q8ITP4
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2M ammonium sulfate, 20mM sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.00850, 1.00916, 0.8130
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2006 / Details: mirror
RadiationMonochromator: Si [111] horizontally focussing / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00851
21.009161
30.8131
ReflectionResolution: 2.44→40 Å / Num. all: 24890 / Num. obs: 24772 / % possible obs: 99.5 % / Observed criterion σ(I): -2 / Redundancy: 9.4 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.4
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2378 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.44→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.919 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Individual isotropic / Cross valid method: R-free / σ(F): 0 / σ(I): -2 / ESU R: 0.28 / ESU R Free: 0.251 / Stereochemistry target values: Engh & Huber
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS; TLS GROUPS WERE GENERATED BY THE TLSMD SERVER; MISSING RESIDUES: 222-225 (CHAIN A), 1-8, 135-139, 222-225 (CHAIN B).
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1256 5.1 %RANDOM
Rwork0.1909 ---
all0.1945 23459 --
obs0.1945 23459 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.44→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 50 92 3491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223381
X-RAY DIFFRACTIONr_bond_other_d0.0010.022261
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9784590
X-RAY DIFFRACTIONr_angle_other_deg2.7043.0035511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.385428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91825134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.17115564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8931512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023704
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02636
X-RAY DIFFRACTIONr_nbd_refined0.2340.2678
X-RAY DIFFRACTIONr_nbd_other0.2390.22194
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21630
X-RAY DIFFRACTIONr_nbtor_other0.1030.21885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.28
X-RAY DIFFRACTIONr_mcbond_it1.7581.52729
X-RAY DIFFRACTIONr_mcbond_other0.2491.5869
X-RAY DIFFRACTIONr_mcangle_it1.9272.53458
X-RAY DIFFRACTIONr_scbond_it4.36651439
X-RAY DIFFRACTIONr_scangle_it6.467101131
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 98 -
Rwork0.25 1645 -
obs--97.21 %
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)
132.6295-27.8815-8.695928.94835.596614.0501-0.4266-0.7164-2.71980.97520.75962.1371-0.5275-0.6933-0.3330.1974-0.0689-0.21770.2820.07410.66895.826834.723236.066
221.2122-5.488-7.48752.70252.86323.31152.0959-0.5172-1.2017-1.2111-1.63871.42150.1128-2.4949-0.45730.28920.1774-0.32430.3267-0.29740.407615.392430.781329.6787
32.38621.11520.54571.91991.79441.8189-0.09340.0366-0.2527-0.0424-0.12650.27130.22790.30510.220.04710.12480.05610.1542-0.03080.130126.477936.732643.5518
45.44322.3531-0.51417.39730.28280.0885-0.1277-0.41620.00750.3206-0.1662-0.1195-0.04070.10640.29390.05840.11390.00810.23870.08140.035640.505240.401543.124
514.5206-5.123-9.750423.163311.515310.7526-0.1161-0.0983-1.8543-1.20720.474-0.23270.65020.9546-0.35790.2771-0.06550.30770.37840.03520.5956.054435.899333.7739
651.671633.64466.533225.1715-3.323918.4152-1.26183.4131-3.5633-2.17081.1497-2.4682.83260.94650.11210.66310.07820.09940.3644-0.09330.392163.690536.978929.1947
79.29971.88722.13784.04851.08224.76990.1909-0.5653-0.138-0.0028-0.2443-0.3913-0.4716-0.0990.05340.06190.00920.05750.06380.05980.062739.382142.817137.1729
816.89157.4086.535925.21531.41512.68990.0069-0.3427-1.634-1.2534-0.44510.77511.2054-0.51630.43820.30860.0729-0.01550.1287-0.15620.234623.9325.833528.1716
917.22349.05553.224712.82442.61370.70830.40540.21820.35420.1598-0.2289-0.006-0.1554-0.0022-0.17650.18970.10680.07660.16460.0055-0.017535.490743.933930.8784
1026.18930.6235-8.74070.03950.11637.19150.1663-0.44311.18510.2050.19960.0648-0.02930.158-0.36580.0645-0.10820.0810.0586-0.00780.27756.253545.22337.8845
117.5011-6.44536.341413.5132-4.30495.5251-0.22710.21990.10620.1051-0.026-0.63180.65540.80620.25320.1022-0.01560.08290.14060.03110.141366.756544.819837.1472
122.2506-1.29220.60211.4670.05441.96860.33780.02310.2511-0.1055-0.57030.37120.17690.23520.23250.14060.11060.1770.12770.02640.045737.649837.951232.048
1314.9091-7.9820.68374.2733-0.3660.03140.3871-2.4452-1.70431.76240.40240.56142.47481.0252-0.78950.8548-0.290.26720.50840.0150.792422.792315.656346.0834
146.21824.204-6.492411.8305-7.976911.8475-0.24690.5612-0.522-0.4724-0.1017-0.23050.4826-0.10450.34870.05270.05380.0920.0473-0.0690.039634.305330.09230.6633
1532.881517.275515.535110.96613.24821.029-0.1504-0.83010.16680.1301-0.0087-0.11370.2872-0.93060.15910.16770.05730.09850.06910.19710.282351.152751.628730.6893
165.44573.161-4.54832.34330.04317.95530.00610.03610.4521-0.2833-0.05170.0002-0.153-0.13980.04560.0238-0.09110.05660.1747-0.00230.109865.018951.0329.5151
1750.70789.3933-23.06951.7412-4.372719.3353-0.7841.8602-0.9239-0.49490.50840.02960.9071-1.7610.2756-0.0001-0.19090.04190.2778-0.05480.130959.581943.55921.2781
1813.09296.4806-10.411713.88614.749422.9535-0.09960.7173-0.8077-0.91730.5696-1.3767-0.35710.4244-0.46990.08510.06880.23410.1902-0.02220.124146.692139.054729.2386
191.91441.50281.88558.22240.03752.1527-0.30350.272-0.7088-0.11420.0356-0.3240.3063-0.15720.26790.05980.10830.06530.1348-0.02830.132633.601131.382138.7069
207.8083.97823.668514.92633.624623.82810.2165-1.77662.01120.0734-0.99672.38192.0987-3.65170.78020.2104-0.16720.17540.47460.02490.881119.17624.858643.6372
2131.779914.5751-16.682126.5895-54.3905118.50830.2891-0.30613.1172.75250.4924-2.0927-5.8053-3.1386-0.78151.073-0.0276-0.15080.23550.08350.872569.682174.54147.2763
226.3833-6.85874.141914.9441-1.794717.2016-0.16540.05090.77790.2313-0.6002-1.2256-2.07141.15240.76570.2832-0.1951-0.1280.0835-0.05320.172272.212264.640651.4661
2311.409-3.96736.715912.83360.42864.6202-0.0876-0.81360.07992.5254-0.02770.0862-1.0944-0.00860.11530.7939-0.2767-0.00220.2531-0.2057-0.046466.63557.169163.4685
241.40490.96832.84859.57930.86065.9122-0.1615-0.62180.01961.5269-0.02290.9033-0.4208-0.34110.18440.318-0.1380.20640.2136-0.0230.039562.625248.493859.7422
2557.9883-27.213-44.054658.230280.2821123.49670.54333.2082-1.223-2.0147-0.1061-0.13862.0308-1.4501-0.43720.82960.1694-0.14750.14660.30190.046561.455328.445441.9496
2613.9125-10.4563-7.760149.31024.47384.37290.7596-0.3781-0.5912-0.7868-0.0389-0.5916-0.2116-1.6752-0.72070.178-0.2057-0.13960.24690.31660.086261.519628.083449.2984
273.96061.2621-0.708310.5222-5.00477.54760.0486-0.04840.47760.3392-0.12880.1958-0.79650.20660.08020.1068-0.1573-0.02560.0681-0.0632-0.059969.881954.68548.8334
2811.307410.8064-5.239425.6802-6.06952.50120.2766-0.8507-0.14620.9883-0.43020.418-0.45910.72660.15360.1472-0.1688-0.15710.20480.1414-0.041469.285635.290556.3201
297.19716.3679-0.196616.997-1.91324.8588-0.62470.0058-0.3362-1.35240.2735-0.20010.84460.16380.35120.2465-0.0922-0.00250.12820.19170.075964.322323.481653.1196
306.8703-5.04423.891510.2688-4.44145.2069-0.3735-1.04240.65021.08280.4688-0.3414-0.90350.1675-0.09530.246-0.15760.01830.08050.03650.071367.625153.550946.1901
3117.4572-11.9578-6.132916.05949.667825.84510.75840.50472.38731.0068-1.3169-0.1602-2.0911-2.2280.55850.650.18580.24330.1572-0.11670.660953.710967.871750.211
3238.4989-19.8848-1.31612.94090.76334.99910.2952-0.3374-0.4748-0.2321-0.20890.0745-0.16960.7473-0.0863-0.0154-0.11550.00820.18330.06660.08569.771646.647942.5888
3315.088916.4924-9.266719.7065-12.76669.83280.764-1.6509-0.3518-0.1342-1.6918-0.69320.07542.34020.92780.30350.05070.07840.34420.28390.17374.894327.589554.5433
3432.524118.9048-1.598221.3235-15.345420.18810.60981.1762-2.26330.067-1.1268-2.83761.25672.22390.51690.50250.27840.2280.19950.17940.277974.413717.928652.8296
3516.91736.9286-27.594934.8119-22.350648.82980.53121.221-0.60311.13660.69350.4861-0.2486-0.0072-1.22470.5570.2530.01760.22360.00530.273770.280118.532543.3359
3618.53988.4005-5.89687.2286-11.465524.4707-0.44020.8714-0.2981-1.84770.3581-1.60331.223.09620.08210.35290.11320.18040.264-0.04230.299270.86629.81740.3186
370.46191.6821-3.135218.3384-8.099722.18120.5742-0.09840.518-1.91510.15060.80230.24050.9482-0.72490.1406-0.0787-0.06820.27840.06620.024168.009337.960745.0584
389.4507-0.0269-0.43936.144-7.69329.65670.0861-0.12230.1544-0.55970.23540.3776-0.08240.789-0.32150.2256-0.06590.06020.0848-0.08630.089264.676647.351149.7916
396.088-6.491-0.735224.8565-2.4390.6679-0.7834-0.67211.0091.46830.34890.17790.0241-0.51490.43450.384-0.05770.18180.1396-0.12310.265459.301958.794254.5451
4065.30512.52623.83059.42571.85160.40230.7906-1.09830.99112.3978-2.3517-0.9602-3.4622-0.56241.56111.1671-0.16910.25870.3647-0.430.640560.979570.717556.4448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 121 - 12
2X-RAY DIFFRACTION2AA13 - 1813 - 18
3X-RAY DIFFRACTION3AA19 - 3919 - 39
4X-RAY DIFFRACTION4AA40 - 4840 - 48
5X-RAY DIFFRACTION5AA49 - 5349 - 53
6X-RAY DIFFRACTION6AA54 - 6054 - 60
7X-RAY DIFFRACTION7AA61 - 7661 - 76
8X-RAY DIFFRACTION8AA77 - 9077 - 90
9X-RAY DIFFRACTION9AA91 - 9691 - 96
10X-RAY DIFFRACTION10AA97 - 10597 - 105
11X-RAY DIFFRACTION11AA106 - 114106 - 114
12X-RAY DIFFRACTION12AA115 - 130115 - 130
13X-RAY DIFFRACTION13AA131 - 141131 - 141
14X-RAY DIFFRACTION14AA142 - 155142 - 155
15X-RAY DIFFRACTION15AA156 - 164156 - 164
16X-RAY DIFFRACTION16AA165 - 178165 - 178
17X-RAY DIFFRACTION17AA179 - 188179 - 188
18X-RAY DIFFRACTION18AA189 - 198189 - 198
19X-RAY DIFFRACTION19AA199 - 213199 - 213
20X-RAY DIFFRACTION20AA214 - 221214 - 221
21X-RAY DIFFRACTION21BB9 - 149 - 14
22X-RAY DIFFRACTION22BB15 - 2615 - 26
23X-RAY DIFFRACTION23BB27 - 3527 - 35
24X-RAY DIFFRACTION24BB36 - 4936 - 49
25X-RAY DIFFRACTION25BB50 - 5650 - 56
26X-RAY DIFFRACTION26BB57 - 6257 - 62
27X-RAY DIFFRACTION27BB63 - 9463 - 94
28X-RAY DIFFRACTION28BB95 - 10295 - 102
29X-RAY DIFFRACTION29BB103 - 118103 - 118
30X-RAY DIFFRACTION30BB119 - 130119 - 130
31X-RAY DIFFRACTION31BB131 - 146131 - 146
32X-RAY DIFFRACTION32BB147 - 156147 - 156
33X-RAY DIFFRACTION33BB157 - 165157 - 165
34X-RAY DIFFRACTION34BB166 - 171166 - 171
35X-RAY DIFFRACTION35BB172 - 182172 - 182
36X-RAY DIFFRACTION36BB183 - 189183 - 189
37X-RAY DIFFRACTION37BB190 - 196190 - 196
38X-RAY DIFFRACTION38BB197 - 203197 - 203
39X-RAY DIFFRACTION39BB204 - 214204 - 214
40X-RAY DIFFRACTION40BB215 - 221215 - 221

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