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- PDB-5ysd: Crystal structure of beta-1,2-glucooligosaccharide binding protei... -

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Basic information

Entry
Database: PDB / ID: 5ysd
TitleCrystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose
ComponentsLin1841 protein
KeywordsSUGAR BINDING PROTEIN / solute-binding protein / protein-carbohydrate complex / beta-1 / 2-glucooligosaccharide / sophorooligosaccharide / alpha/beta domain
Function / homology
Function and homology information


maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria innocua serovar 6a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbe, K. / Nakajima, M. / Taguchi, H. / Arakawa, T. / Fushinobu, S.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
Authors: Abe, K. / Sunagawa, N. / Terada, T. / Takahashi, Y. / Arakawa, T. / Igarashi, K. / Samejima, M. / Nakai, H. / Taguchi, H. / Nakajima, M. / Fushinobu, S.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin1841 protein
B: Lin1841 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,78810
Polymers89,1642
Non-polymers1,6248
Water5,152286
1
A: Lin1841 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4656
Polymers44,5821
Non-polymers8835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-28 kcal/mol
Surface area17270 Å2
MethodPISA
2
B: Lin1841 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3234
Polymers44,5821
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-12 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.082, 125.561, 91.780
Angle α, β, γ (deg.)90.00, 101.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A7 - 392
2010B7 - 392

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Components

#1: Protein Lin1841 protein / beta-1 / 2-glucooligosaccharide binding protein


Mass: 44582.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin1841 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92AS8
#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.15M MES-NaOH, pH 5.5, 50% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 44909 / % possible obs: 96.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.071 / Net I/σ(I): 12.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.639 / Num. unique obs: 2234 / CC1/2: 0.697 / Rpim(I) all: 0.389 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
MOLREPphasing
Cootrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YSE
Resolution: 2.1→44.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20732 2264 5 %RANDOM
Rwork0.16942 ---
obs0.17139 42614 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.682 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 109 286 6530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026407
X-RAY DIFFRACTIONr_bond_other_d00.025828
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9738687
X-RAY DIFFRACTIONr_angle_other_deg3.704313643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63125.804286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9681512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216994
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021222
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_it0.8721.4653107
X-RAY DIFFRACTIONr_mcbond_other0.8711.4653106
X-RAY DIFFRACTIONr_mcangle_it1.442.1933882
X-RAY DIFFRACTIONr_mcangle_other1.442.1933883
X-RAY DIFFRACTIONr_scbond_it1.1971.6443300
X-RAY DIFFRACTIONr_scbond_other1.1971.6453301
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.932.4034806
X-RAY DIFFRACTIONr_long_range_B_refined4.10217.6527263
X-RAY DIFFRACTIONr_long_range_B_other4.10317.6577264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25838 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 165 -
Rwork0.228 3081 -
obs--95.16 %
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)
12.86131.11751.486510.31612.17616.4571-0.1551-0.10350.20190.34630.3464-0.1335-0.04920.3556-0.19130.0415-0.01870.00490.20910.00320.16743.6218.0719.06
22.2143-1.7747-0.07235.2156-7.385810.58590.3016-0.0710.2531-0.68470.087-0.40010.41620.3933-0.38860.0752-0.01890.06220.1881-0.00910.19533.74119.2150.123
30.85230.20750.27659.1465-3.48813.96310.06870.012-0.03450.0364-0.3372-0.6895-0.14320.33230.26860.0391-0.02960.04420.16820.03580.17254.24419.1487.7
43.89358.00642.449821.49165.61487.3147-0.0756-0.26550.43640.5132-0.37080.4991-0.68180.62340.44640.4187-0.0671-0.04420.2887-0.04910.2060.69914.07424.207
50.15460.57710.25854.3483-0.58291.54740.075-0.01680.02150.7856-0.02150.229-0.1913-0.0639-0.05360.229-0.00590.10460.1955-0.01970.1852-7.48814.17317.57
60.6085-1.3639-3.3967.75153.742122.92850.1640.1220.0407-0.3831-0.01980.4021-0.9345-0.7797-0.14420.0590.0747-0.02110.22120.04840.4105-17.20823.3456.171
70.08090.3275-0.00472.96750.20560.81990.01140.05220.04440.1409-0.05990.4296-0.0175-0.10560.04860.0413-0.0150.04110.18690.00130.1776-10.853.325.76
88.2884-1.5325-3.26822.04264.26569.0386-0.04270.2092-0.086-0.0446-0.10590.09290.0767-0.26040.14860.2427-0.0251-0.00940.14010.00740.184-7.138-21.781-1.839
91.1679-0.9208-0.96194.57481.64231.3611-0.04310.005-0.05830.21030.0478-0.24130.10430.0814-0.00470.0665-0.00360.01490.16760.02410.1137-0.62-18.1048.427
101.4891-0.26921.38264.3981-0.11897.0011-0.0464-0.16060.00750.7198-0.02830.5358-0.2047-0.64320.07470.1481-0.00930.13780.2172-0.00440.1957-17.405-10.97721.631
111.1686-0.31730.13611.7478-0.68090.902-0.0156-0.0344-0.00550.0946-0.0386-0.1460.03310.12790.05410.0437-0.01070.03020.1618-0.0060.12762.522-14.8948.453
127.12962.0317-1.99257.76522.85975.09720.00540.28020.1538-0.5256-0.0916-0.3801-0.01010.16380.08610.09590.02480.04960.19960.08190.13564.22-6.987-5.594
1310.79041.4877-7.19274.9529-3.91117.3677-0.04030.1162-0.0099-0.06490.01810.19440.2274-0.24380.02230.0566-0.02480.0270.197-0.02830.1576-14.876-13.6175.786
141.44382.9272-0.120912.85311.49121.06230.151-0.1890.1130.5129-0.09790.2913-0.1990.041-0.05310.1248-0.00720.07060.1914-0.02310.1292-6.53716.34214.261
154.70315.20694.490111.42236.315910.0891-0.16510.13330.3115-0.1138-0.06730.6392-0.72170.10230.23240.08270.02010.02350.13530.01660.1874-6.57424.0355.381
163.3938-1.01160.30675.9283-0.49842.47660.02190.22990.3121-0.5872-0.08990.24040.02970.0830.0680.0970.0001-0.01760.17480.06060.1356-7.7679.546-3.762
1719.11610.39670.543621.8758.951710.8506-0.21290.9307-0.28560.1820.584-0.95050.49610.3059-0.3710.1910.0033-0.07440.18050.01310.1536-10.8886.067-11.262
181.6092-0.0845-0.78622.3025-0.58289.35450.09340.163-0.0841-0.4404-0.16450.4206-0.3052-0.26570.0710.13580.0232-0.04480.184-0.00080.1912-11.995-2.623-3.816
191.38650.17830.18653.3466-1.160.74880.124-0.108-0.05050.646-0.10290.0136-0.12660.0698-0.0210.2355-0.02190.05540.1752-0.01020.0773-5.748-8.58224.122
207.3311-12.4603-4.989723.87799.00183.65070.1695-0.39950.3335-0.03120.0485-0.39360.002-0.1309-0.21810.5341-0.08910.1310.7062-0.00270.2353-13.91.0833.593
212.520.1837-0.67564.9280.82326.249-0.0484-0.07550.17410.63720.0636-0.71010.78160.5804-0.01510.4790.0193-0.07080.23640.04930.1591-3.685-67.28840.173
221.48632.0502-2.708714.9557-8.09616.7738-0.092-0.0887-0.01811.1441-0.2165-0.8021-0.01530.25550.30850.43440.0008-0.1020.20120.03150.109-3.369-68.21839.432
233.271-0.4651.08462.3106-2.83433.65340.13050.11120.0045-0.4142-0.1924-0.16840.67020.30860.06190.52520.0898-0.02990.34980.0090.4315-2.085-64.9525.817
240.40980.5898-1.00924.0805-1.3013.81110.04770.04310.0422-0.1710.02020.12540.5286-0.2602-0.06790.3588-0.0564-0.02280.23850.00670.1683-12.953-63.9224.263
2513.8451-6.3041-10.345717.085920.864535.5122-0.2624-0.0751-0.68060.73640.07240.96741.2244-0.77840.190.371-0.2010.05570.48810.08920.3037-24.421-72.64333.941
265.449-2.41660.13163.82-1.215811.35960.14930.1398-0.17580.3093-0.32220.6460.3586-1.05060.1730.2126-0.15070.07680.3608-0.02810.2777-24.182-61.84134.745
273.36161.46796.835711.46099.847718.55620.0737-0.005-0.0821-0.5629-0.26040.8226-0.2672-0.4870.18670.1876-0.0398-0.04760.42570.11910.3402-20.597-61.44823.759
280.08060.10850.06656.57481.43821.45320.0149-0.1161-0.02980.5582-0.02030.1029-0.1408-0.08680.00530.3042-0.04310.06250.24420.01230.1022-13.141-45.54140.945
294.12642.54073.65785.03438.528916.09810.1932-0.2972-0.09490.4708-0.430.3883-0.2404-0.76050.23680.82490.03990.32670.2251-0.03390.2805-16.319-27.22943.849
300.44520.3137-0.08683.08240.2622.4617-0.0172-0.0405-0.04360.4129-0.065-0.109-0.28840.04390.08210.1873-0.00760.01790.14620.01480.0955-8.072-34.12332.656
315.005-2.1442-0.45628.88611.13180.28170.1495-0.2524-0.19931.5015-0.2119-0.31750.0290.0460.06240.7374-0.0834-0.04590.28720.11190.1606-8.227-42.02551.506
321.0245-2.47840.12277.4963-0.331.57880.20810.0209-0.1485-0.2715-0.27320.59670.2601-0.18810.06510.1913-0.06750.02850.2020.00560.1291-14.059-57.35630.914
333.022-6.5682-3.810614.40168.34315.4084-0.3969-0.1786-0.23081.0520.40250.62351.1663-0.0664-0.00550.9085-0.2309-0.14550.40250.14530.4422-15.453-69.91741.983
343.3013-0.34225.710610.70141.953311.04460.069-0.4219-0.22551.2872-0.04110.46370.1506-0.5257-0.02790.4872-0.12990.06470.41440.13650.255-15.596-57.05746.582
359.24213.29870.771114.2687.385715.79310.3565-0.3546-0.16550.9414-0.18360.5210.2693-1.1379-0.17280.2927-0.10120.16790.3150.10540.2114-24.935-56.09347.049
361.57810.369-4.06128.1624-0.980311.14390.0886-0.07660.05991.4137-0.11950.5853-0.3835-0.3120.03090.5773-0.01280.1660.5064-0.06190.289-20.697-45.68647.598
3719.6682-1.569-2.17028.01123.46110.13250.3549-0.196-0.67870.6431-0.41820.25040.4619-1.23660.06340.1444-0.03220.09830.29330.02070.1626-23.426-45.87435.456
381.47531.11790.37975.5347-0.70181.28980.04970.03910.0036-0.1453-0.1538-0.2414-0.00430.06980.10420.11060.02190.05550.15690.02330.0951-5.339-40.60520.447
397.49967.5745.116417.685212.32788.60020.23660.2288-0.2007-0.1229-0.0418-0.2971-0.0942-0.0354-0.19470.20040.04510.06440.1862-0.00580.1801-8.165-47.2699.977
4012.55697.51316.583117.55747.7927.8841-0.29840.30920.162-0.79110.46410.1955-0.8423-0.1314-0.16570.1310.01980.01530.1738-0.04440.2146-11.611-57.9854.046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 48
2X-RAY DIFFRACTION2A49 - 55
3X-RAY DIFFRACTION3A56 - 74
4X-RAY DIFFRACTION4A75 - 86
5X-RAY DIFFRACTION5A87 - 110
6X-RAY DIFFRACTION6A111 - 121
7X-RAY DIFFRACTION7A122 - 158
8X-RAY DIFFRACTION8A159 - 171
9X-RAY DIFFRACTION9A172 - 203
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