[English] 日本語
Yorodumi
- PDB-6am8: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6am8
TitleEngineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9 with Trp bound as E(Aex2)
Components(Tryptophan synthase beta chain ...) x 2
KeywordsBIOSYNTHETIC PROTEIN / PLP Type II / Tryptophan Synthase / Engineered / Allostery
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / cytoplasm
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PLT / TRYPTOPHAN / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBuller, A.R. / van Roye, P.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble.
Authors: Buller, A.R. / van Roye, P. / Cahn, J.K.B. / Scheele, R.A. / Herger, M. / Arnold, F.H.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,59013
Polymers174,0194
Non-polymers1,5719
Water7,332407
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8977
Polymers87,0092
Non-polymers8885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-39 kcal/mol
Surface area24460 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6936
Polymers87,0092
Non-polymers6844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-35 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.233, 106.036, 158.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Tryptophan synthase beta chain ... , 2 types, 4 molecules ADBC

#1: Protein Tryptophan synthase beta chain 1


Mass: 43618.719 Da / Num. of mol.: 2
Mutation: I16V, E17G, I68V, F95L, F274S, T292S, T321A, V384A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U093, tryptophan synthase
#2: Protein Tryptophan synthase beta chain 1


Mass: 43390.602 Da / Num. of mol.: 2
Mutation: I16V, E17G, I68V, F95L, F274S, T292S, T321A, V384A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U093, tryptophan synthase

-
Non-polymers , 4 types, 416 molecules

#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PLT / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-L-TRYPTOPHANE


Mass: 433.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N3O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350 and 0.1 M Na HEPES pH 7.85

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.83→40 Å / Num. obs: 121628 / % possible obs: 99.2 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rpim(I) all: 0.036 / Net I/σ(I): 11.5
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 24562 / CC1/2: 0.597 / Rpim(I) all: 0.864 / % possible all: 88.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VM5
Resolution: 1.83→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.655 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23141 6031 5 %RANDOM
Rwork0.20155 ---
obs0.20307 115028 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.626 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å20 Å2
2---0.42 Å20 Å2
3----3.02 Å2
Refinement stepCycle: 1 / Resolution: 1.83→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11487 0 109 407 12003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01912059
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211493
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9716353
X-RAY DIFFRACTIONr_angle_other_deg0.779326343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95751569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67524.029484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4151924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1911557
X-RAY DIFFRACTIONr_chiral_restr0.0590.21799
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022716
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_it0.2731.3676250
X-RAY DIFFRACTIONr_mcbond_other0.2741.3676250
X-RAY DIFFRACTIONr_mcangle_it0.4962.0437808
X-RAY DIFFRACTIONr_mcangle_other0.4962.0447809
X-RAY DIFFRACTIONr_scbond_it0.2081.3845809
X-RAY DIFFRACTIONr_scbond_other0.2071.3835805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3772.0758533
X-RAY DIFFRACTIONr_long_range_B_refined5.36211.43613747
X-RAY DIFFRACTIONr_long_range_B_other5.32711.16513609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 410 -
Rwork0.384 7352 -
obs--86.54 %
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)
11.25170.3441-0.33712.57340.16755.2886-0.15280.389-0.219-0.80920.11070.01410.9667-0.04950.04210.4631-0.06540.02880.3792-0.10890.1255-4.605-48.139-3.176
21.05820.1382-0.2062.0635-0.10172.382-0.0290.0583-0.0194-0.0079-0.03580.09460.0974-0.15310.06480.1182-0.00620.01040.4291-0.01270.2513-9.627-36.15621.634
32.5957-1.0551.57112.5868-2.34813.3607-0.2090.0589-0.20450.00060.0729-0.0480.3236-0.08420.13610.2352-0.02640.0760.3007-0.03460.222-1.149-51.26515.307
44.12573.7411-2.58647.943-2.60823.2655-0.11490.03920.09730.3525-0.0947-0.59060.13560.57240.20960.14940.1039-0.00380.33380.07720.309912.294-46.98216.733
52.8802-2.56431.6992.7336-1.69553.24960.02050.60380.2385-0.371-0.7296-0.67710.76420.97730.70910.44340.27370.46920.55040.30950.573710.381-50.49511.333
60.7658-0.1697-0.12711.02110.22862.03-0.02210.13460.0179-0.1719-0.0270.0304-0.0632-0.11320.04910.1289-0.0030.01580.3977-0.010.2169-6.423-32.74310.032
73.35112.13240.587910.99232.52335.4230.01120.20010.2037-0.1941-0.0279-0.2387-0.22070.21010.01670.1944-0.01930.05380.3910.01640.19145.37-33.66-2.586
81.6091-0.4029-4.17610.297-0.494830.4089-0.03190.30210.0631-0.2054-0.3312-0.07891.15720.26370.3630.51020.1130.0970.7571-0.03570.253914.729-33.61-3.762
90.98050.0007-0.26370.85710.33362.45980.02280.07130.1038-0.1257-0.0045-0.1217-0.26650.1766-0.01830.1037-0.03390.03190.3730.02140.22822.685-26.56113.155
103.0823-1.32751.07182.9829-0.60572.7790.01080.05850.25790.0767-0.0906-0.2388-0.37360.23170.07980.1767-0.07310.02630.3948-0.00410.22760.212-23.81720.776
110.27-0.1162-0.48172.2832-0.42141.80840.0023-0.19840.08730.507-0.0053-0.0265-0.1660.04570.0030.25610.0092-0.0410.4213-0.03290.1653-6.375-28.84962.136
120.8287-0.9606-0.17762.3383-0.06391.97560.03050.0115-0.0049-0.1059-0.12270.08650.156-0.09750.09230.107-0.03380.00330.4088-0.00660.2502-11.211-39.88636.457
131.85840.6825-0.50782.2310.04181.7881-0.01080.11780.1160.0286-0.0352-0.0197-0.1268-0.04150.0460.1496-0.0054-0.0120.37220.00370.2157-1.732-26.70343.483
141.3466-1.15750.34933.9434-1.04462.91610.0117-0.0210.0094-0.0659-0.0766-0.35310.00410.47590.06490.0966-0.0184-0.00520.40570.02360.268710.875-30.85140.138
151.16290.417-1.18453.1670.06883.87850.0751-0.2315-0.06080.5655-0.2281-0.439-0.23070.79190.1530.1285-0.0627-0.08820.43120.02760.22579.854-27.37850.907
160.76670.55680.20742.30.86541.8254-0.131-0.0195-0.01420.01060.03750.0697-0.0118-0.1370.09350.1618-0.00610.01530.38920.01160.2426-9.847-36.32547.271
173.1932-0.78710.05621.7065-0.12291.6873-0.1251-0.1333-0.10130.24380.06490.12220.3857-0.16340.06020.2711-0.03520.02850.34570.02340.1927-9.486-49.44348.383
183.7939-1.8944-1.30682.40591.05044.2112-0.0627-0.4023-0.01870.28710.0309-0.26880.40540.52710.03180.27280.0752-0.07790.42640.06030.12087.326-45.43861.129
190.6649-0.1259-0.09240.83970.41732.4425-0.0315-0.0077-0.15690.1156-0.0092-0.03830.5420.0250.04070.23320.04570.00580.31410.03590.2107-1.099-51.9744.08
209.6825-0.90972.01585.89930.06063.8203-0.02210.2463-0.4136-0.0391-0.006-0.54220.41630.71220.0280.2780.0340.02550.38810.00450.271612.651-46.09134.511
212.0292-0.96650.77052.0574-0.45682.7544-0.1759-0.4260.09940.49920.17360.0903-0.2674-0.28780.00220.18270.04010.03380.4215-0.00020.1666-53.173-66.71161.278
221.547-1.0508-0.06443.0027-0.16942.6935-0.0080.0723-0.0047-0.1399-0.01170.11470.2507-0.05660.01960.1637-0.01920.00050.4180.01310.2552-49.615-76.58434.535
231.45141.2097-0.3394.2797-3.00732.3716-0.05740.01130.15210.19610.02060.0118-0.225-0.08390.03680.19150.01690.00260.343-0.00490.2276-45.896-60.16544.995
2410.483-9.065410.411620.3887-1.296815.12020.76090.56580.7435-0.6123-0.4626-2.5080.83410.7164-0.29830.09650.10070.15340.60930.31140.6452-28.319-64.60643.328
253.00852.0572-0.60352.155-1.78827.1376-0.1147-0.3336-0.42360.1378-0.5528-0.6548-0.38671.10250.66750.2437-0.1341-0.15830.410.21630.4511-32.695-58.85244.404
264.1975-0.6793-1.57068.1583-1.49361.32790.0028-0.29440.27281.1857-0.1033-0.19-0.56110.11650.10050.5459-0.0334-0.1070.2992-0.05890.1817-42.347-57.35857.139
270.685-0.34420.13071.2411-0.29521.68080.044-0.0496-0.09310.0005-0.02950.10210.2459-0.0936-0.01450.1437-0.00880.00780.35920.01250.2486-49.186-80.74446.19
284.125-2.0365-0.53691.05510.36015.1394-0.1275-0.35330.03240.13020.0979-0.09590.1660.44670.02970.2526-0.0252-0.08120.39970.06320.1894-33.677-78.04361.712
290.995-0.12310.21421.37920.00172.07060.11510.0714-0.0944-0.0001-0.1156-0.11910.31920.22190.00050.11610.07180.00060.35480.0310.2247-37.055-84.36843.952
3011.0919-2.79021.46538.5117-2.00293.45970.22140.1710.0227-0.1606-0.133-0.6881-0.18150.6747-0.08840.296-0.01460.07260.39360.03850.277-24.753-72.74836.045
310.70740.8967-0.42782.33650.11923.1982-0.05970.0952-0.1524-0.538-0.10330.04920.45950.15650.1630.48470.1702-0.04670.4463-0.07310.124-38.04-76.729-3.1
320.8032-0.3031-0.09782.5748-0.08292.2960.00250.0123-0.0482-0.0836-0.01490.11410.2282-0.06570.01240.13490.00940.00220.43410.00520.2195-47.896-70.94520.611
332.38840.24621.87022.9149-1.871611.282-0.06050.0427-0.2124-0.09890.02310.0525-0.10880.11280.03740.23760.1020.03060.3323-0.00070.1707-33.108-80.52415.325
344.12291.0939-1.07074.7989-1.57990.6629-0.09290.06730.2517-0.04870.1084-0.12360.04170.0402-0.01560.24090.02920.05120.5954-0.01130.0683-24.949-71.54820.726
354.95220.54113.34236.6579-5.21298.40560.16440.96450.3103-0.0914-1.4482-1.1477-0.29032.43271.28370.22430.01130.00330.97950.36080.2349-24.201-75.868.505
360.7823-0.1112-0.73551.15650.57932.1974-0.09220.1217-0.0894-0.29120.07080.070.36820.03870.02140.23150.02910.00670.41660.00060.1607-43.724-73.2439.476
372.47340.82310.31011.9528-0.04592.32540.00370.15420.0593-0.21680.02560.0584-0.1751-0.0831-0.02930.18540.0447-0.00020.42390.02710.1866-47.201-58.19611.062
382.07192.62680.41965.83143.77145.43140.11610.2610.0773-0.34850.1856-0.3363-0.4890.6139-0.30180.23630.0430.16680.59610.15040.1654-30.669-58.276-0.784
390.6989-0.01760.10281.21410.20232.75840.02940.0790.0873-0.162-0.0298-0.1075-0.26030.09660.00040.1243-0.01870.02190.37740.02960.2096-40.293-55.80615.186
403.4936-1.461.162.5323-0.21222.7764-0.08260.08120.23560.2170.012-0.1239-0.32560.06070.07060.2017-0.01960.01680.34730.01860.2145-43.964-55.13722.442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 28
2X-RAY DIFFRACTION2A29 - 83
3X-RAY DIFFRACTION3A84 - 122
4X-RAY DIFFRACTION4A123 - 140
5X-RAY DIFFRACTION5A141 - 178
6X-RAY DIFFRACTION6A179 - 264
7X-RAY DIFFRACTION7A265 - 282
8X-RAY DIFFRACTION8A283 - 292
9X-RAY DIFFRACTION9A293 - 352
10X-RAY DIFFRACTION10A353 - 384
11X-RAY DIFFRACTION11B1 - 27
12X-RAY DIFFRACTION12B28 - 80
13X-RAY DIFFRACTION13B81 - 121
14X-RAY DIFFRACTION14B122 - 145
15X-RAY DIFFRACTION15B146 - 177
16X-RAY DIFFRACTION16B178 - 216
17X-RAY DIFFRACTION17B217 - 256
18X-RAY DIFFRACTION18B257 - 292
19X-RAY DIFFRACTION19B293 - 374
20X-RAY DIFFRACTION20B375 - 385
21X-RAY DIFFRACTION21C1 - 29
22X-RAY DIFFRACTION22C30 - 80
23X-RAY DIFFRACTION23C81 - 129
24X-RAY DIFFRACTION24C130 - 140
25X-RAY DIFFRACTION25C141 - 161
26X-RAY DIFFRACTION26C162 - 180
27X-RAY DIFFRACTION27C181 - 255
28X-RAY DIFFRACTION28C256 - 290
29X-RAY DIFFRACTION29C291 - 374
30X-RAY DIFFRACTION30C375 - 387
31X-RAY DIFFRACTION31D1 - 29
32X-RAY DIFFRACTION32D30 - 92
33X-RAY DIFFRACTION33D93 - 122
34X-RAY DIFFRACTION34D123 - 146
35X-RAY DIFFRACTION35D147 - 177
36X-RAY DIFFRACTION36D178 - 212
37X-RAY DIFFRACTION37D213 - 265
38X-RAY DIFFRACTION38D266 - 292
39X-RAY DIFFRACTION39D293 - 353
40X-RAY DIFFRACTION40D354 - 384

+
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://pdbjlvh1.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