[English] 日本語
Yorodumi
- PDB-6u6c: Crystal structure of tryptophan synthase from M. tuberculosis - a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u6c
TitleCrystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK2-bound form
Components(Tryptophan synthase ...) x 2
KeywordsLyase/Lyase Inhibitor / PLP / HETEROTETRAMER / AMINO ACID BIOSYNTHESIS / SUBSTRATE CHANNELING / LYASE-LYASE INHIBITOR COMPLEX / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / 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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / 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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / ALANINE / FORMIC ACID / : / MALONATE ION / Chem-P1T / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-PZV / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsChang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
Global Health Innovative Technology Fund United States
CitationJournal: Protein Sci. / Year: 2020
Title: Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase.
Authors: Michalska, K. / Chang, C. / Maltseva, N.I. / Jedrzejczak, R. / Robertson, G.T. / Gusovsky, F. / McCarren, P. / Schreiber, S.L. / Nag, P.P. / Joachimiak, A.
History
DepositionAug 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,001163
Polymers287,6568
Non-polymers11,345155
Water21,5281195
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,11278
Polymers143,8284
Non-polymers5,28474
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21190 Å2
ΔGint22 kcal/mol
Surface area41530 Å2
MethodPISA
2
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,88985
Polymers143,8284
Non-polymers6,06181
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint33 kcal/mol
Surface area40870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.106, 159.226, 164.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Tryptophan synthase ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Tryptophan synthase alpha chain


Mass: 28579.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 43334.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase

-
Non-polymers , 13 types, 1350 molecules

#3: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 92 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical
ChemComp-PZV / 1-(2-fluorobenzene-1-carbonyl)-N-methyl-2,3-dihydro-1H-indole-5-sulfonamide


Mass: 334.365 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H15FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#11: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#12: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#13: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#14: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1195 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M sodium malonate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 138216 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.089 / Rrim(I) all: 0.321 / Χ2: 0.891 / Net I/σ(I): 3 / Num. measured all: 1758336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4410.71.64968450.6610.5271.7330.75499.7
2.44-2.4911.41.50768760.7090.4641.5780.7799.9
2.49-2.5311.91.41468290.7510.4251.4780.7499.9
2.53-2.5912.31.28168240.7720.3761.3360.81299.8
2.59-2.6412.61.23868740.8020.361.290.74999.9
2.64-2.712.61.14368800.8310.3311.1910.74999.9
2.7-2.7712.30.95668360.8590.280.9970.75599.8
2.77-2.8511.80.82468250.8570.2480.8620.86899.2
2.85-2.9313.70.78268710.9330.2170.8120.77799.8
2.93-3.0213.60.6568880.950.180.6750.77299.8
3.02-3.1313.60.51768950.9620.1440.5370.78299.8
3.13-3.2613.50.40468740.9750.1130.420.793100
3.26-3.413.30.30868960.9830.0870.320.82399.8
3.4-3.5812.80.23569280.9880.0680.2450.85199.9
3.58-3.8112.40.17668710.9920.0510.1840.89898.9
3.81-4.113.90.14769590.9940.0410.1520.98499.8
4.1-4.5113.60.11469420.9960.0320.1181.04199.7
4.51-5.16130.10269940.9960.0290.1061.04299.7
5.16-6.4912.70.11770150.9940.0340.1221.13799.1
6.49-3012.60.06772940.9950.020.071.61599.5

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DWE

6dwe


Resolution: 2.402→29.876 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1951 2691 1.95 %
Rwork0.1529 --
obs0.1537 138098 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.74 Å2 / Biso mean: 31.1161 Å2 / Biso min: 4.77 Å2
Refinement stepCycle: final / Resolution: 2.402→29.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19188 0 732 1195 21115
Biso mean--50.21 36.5 -
Num. residues----2609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.402-2.44540.24971450.222683397
2.4454-2.49240.27281220.20957143100
2.4924-2.54330.27171210.20387068100
2.5433-2.59850.2721420.19797061100
2.5985-2.6590.23941360.19657128100
2.659-2.72540.2611270.19197085100
2.7254-2.7990.26411330.19117068100
2.799-2.88130.22411580.1827070100
2.8813-2.97430.22881350.17977089100
2.9743-3.08050.23151450.17477110100
3.0805-3.20370.24931580.1747122100
3.2037-3.34930.20911640.15987089100
3.3493-3.52560.19421480.14597142100
3.5256-3.74610.16331500.135709799
3.7461-4.03470.16611540.12287150100
4.0347-4.43960.1551480.1127198100
4.4396-5.07930.13121240.1087213100
5.0793-6.3890.16151540.1381723699
6.389-29.8760.14071270.1364750599
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)
10.0013-0.0006-0.00030.0016-0.00110.001-0.0090.00910.0022-0.0231-0.0084-0.0231-0.00040.0029-00.21720.07990.05950.37770.02950.321594.9542-12.24644.6167
20.0195-0.01350.02010.0172-0.01430.01790.05840.0197-0.01770.0394-0.0057-0.07640.00990.005300.0961-0.0073-0.00340.15860.02350.23787.7558-13.790125.66
30.00860.0080.0020.00630.00020.0039-0.02270.04950.0380.02030.0154-0.0374-0.03860.05500.0902-0.02680.01450.16650.0290.250287.3285-1.6721.1298
40.0134-0.00660.00710.00770.00130.00980.06840.13060.00240.0062-0.0217-0.09690.0275-0.0196-00.14640.01780.03360.27010.04180.224679.2346-8.2648.9292
50.00080.00190.00190.00420.00430.00380.00740.132-0.10240.0104-0.0366-0.01370.0364-0.003700.18570.0390.00140.2663-0.09580.297684.1824-24.41938.158
60.004-0.00630.0010.0068-0.00120.0003-0.01640.0516-0.0710.0305-0.0636-0.03140.04610.032100.16530.04730.00170.19670.00380.363693.2899-23.954421.0107
70.0010.0013-0.00230.0003-0.00230.00990.04390.03490.0026-0.02870.0278-0.0157-0.0193-0.0034-00.18980.01930.0350.22130.05790.194558.6190.429912.485
80.00380.00370.00730.00620.00910.01420.04530.02660.0063-0.03760.03350.0391-0.03460.0142-00.10720.00270.00560.1370.00880.105647.5629-12.88811.6568
90.03240.0371-0.04490.0833-0.03880.0650.0490.0032-0.0007-0.0248-0.0487-0.0116-0.0227-0.00020.00080.08110.00680.00850.08660.00480.085449.1053-9.578927.8302
100.05460.011-0.02280.04120.04290.04680.0356-0.03220.01020.0236-0.0047-0.0412-0.08690.004800.0869-0.00870.00730.08550.00530.074653.89942.444136.3558
110.02560.00840.01310.0394-0.0360.05080.0116-0.07560.01660.0862-0.0430.0565-0.0477-0.0414-0.05520.3937-0.00350.19860.2645-0.04130.21245.3439-27.466185.1029
120.0184-0.0115-0.00540.11340.00830.00320.0201-0.0383-0.03550.2332-0.03950.1254-0.0527-0.0018-0.01430.2105-0.12410.13250.11630.03220.144712.3114-33.86974.2994
130.0704-0.01740.03240.04790.00240.01780.0199-0.0388-0.04160.02780.0070.0776-0.0896-0.03340.05080.2192-0.01640.14910.1959-0.0240.24891.5514-21.51770.5498
140.0518-0.01920.00790.03690.00470.00330.0975-0.10820.06150.2126-0.02470.0206-0.0341-0.02120.06860.5448-0.07290.13380.2004-0.09070.156912.363-19.243386.4745
150.00530.00520.0070.0938-0.03030.0320.05120.0541-0.01560.0449-0.03450.0678-0.0255-0.09060.00180.0516-0.01020.03330.1829-0.01850.15078.2986-15.771649.9165
160.09490.0649-0.05190.1252-0.03570.16020.0110.0075-0.00760.0287-0.0293-0.01180.0334-0.0400.0695-0.01410.0070.08650.00490.090926.2639-22.566842.8421
170.0880.07910.05240.17170.0520.1118-0.21540.1515-0.1119-0.28880.0718-0.07540.1835-0.026-0.26480.4959-0.08580.2030.1789-0.11010.082137.3395-40.0792-45.9691
180.00990.00380.00350.0040.00230.009-0.08510.0088-0.0219-0.0359-0.0435-0.03150.03540.0416-0.00010.38460.00270.1760.28140.00450.334351.0867-35.3921-39.8443
190.0536-0.00560.00020.0042-0.00260.002-0.00750.09660.0127-0.18980.0205-0.04190.040.04590.02420.5474-0.16930.10550.34530.02940.127842.2525-27.8653-55.5499
200.08550.0174-0.18520.0087-0.03820.446-0.00560.00050.00110.0020.00690.0024-0.00310.001500.5845-0.03010.02260.5843-0.01130.566341.2603-26.4798-55.72
210.01090.00360.00640.0070.00390.0028-0.0421-0.0038-0.0033-0.06060.0528-0.05590.08030.099-00.14830.03470.05050.1820.01250.180248.4784-26.6005-19.4006
220.0857-0.096-0.06410.12750.06110.1599-0.0425-0.0062-0.0109-0.0513-0-0.00530.0782-0.0387-0.00060.0801-0.01640.0150.053-0.0120.064729.5668-23.7787-11.9911
230.0207-0.00590.02330.0793-0.03190.03580.0970.0012-0.0226-0.0348-0.01260.18750.0412-0.04550.00730.09640.0223-0.00470.1669-0.02230.2254-20.843514.26349.6404
240.00260.00010.00020.00580.00290.00440.03940.03050.0091-0.0019-0.0170.0277-0.02140.0267-00.13580.03240.02580.1533-0.00580.1842-14.113223.759610.4572
250.0102-0.0012-0.01070.0053-0.00320.0132-0.0044-0.082-0.05480.02250.02920.0554-0.02160.0509-00.1559-0.00060.0340.168-0.00430.1752-9.499514.40222.3958
260.02510.0009-0.01240.0094-0.00760.0085-0.0342-0.0894-0.1286-0.0126-0.02540.21950.0397-0.0191-0.00050.141-0.0223-0.00840.1760.04430.3277-25.57574.817516.9922
270.0011-0.00220.0010.0065-0.00120.00350.0373-0.0289-0.0206-0.00570.0490.0196-0.0150.036800.1782-0.0130.01240.2359-0.03040.174312.817913.307317.9604
280.098-0.0329-0.07630.17630.03410.13520.0322-0.012-0.0151-0.0323-0.03270.005-0.0489-0.0161-00.0605-0.00270.00190.0742-0.01260.058816.56583.31611.55
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 21 )A8 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 85 )A22 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 126 )A86 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 197 )A127 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 231 )A198 - 231
6X-RAY DIFFRACTION6chain 'A' and (resid 232 through 267 )A232 - 267
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 31 )B4 - 31
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 64 )B32 - 64
9X-RAY DIFFRACTION9chain 'B' and (resid 65 through 258 )B65 - 258
10X-RAY DIFFRACTION10chain 'B' and (resid 259 through 408 )B259 - 408
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 37 )C8 - 37
12X-RAY DIFFRACTION12chain 'C' and (resid 38 through 142 )C38 - 142
13X-RAY DIFFRACTION13chain 'C' and (resid 143 through 197 )C143 - 197
14X-RAY DIFFRACTION14chain 'C' and (resid 198 through 267 )C198 - 267
15X-RAY DIFFRACTION15chain 'D' and (resid 4 through 50 )D4 - 50
16X-RAY DIFFRACTION16chain 'D' and (resid 51 through 407 )D51 - 407
17X-RAY DIFFRACTION17chain 'E' and (resid 9 through 142 )E9 - 142
18X-RAY DIFFRACTION18chain 'E' and (resid 143 through 197 )E143 - 197
19X-RAY DIFFRACTION19chain 'E' and (resid 198 through 265 )E198 - 265
20X-RAY DIFFRACTION20chain 'E' and (resid 266 through 266 )E301
21X-RAY DIFFRACTION21chain 'F' and (resid 4 through 50 )F4 - 50
22X-RAY DIFFRACTION22chain 'F' and (resid 51 through 407 )F51 - 407
23X-RAY DIFFRACTION23chain 'G' and (resid 8 through 85 )G8 - 85
24X-RAY DIFFRACTION24chain 'G' and (resid 86 through 126 )G86 - 126
25X-RAY DIFFRACTION25chain 'G' and (resid 127 through 197 )G127 - 197
26X-RAY DIFFRACTION26chain 'G' and (resid 198 through 267 )G198 - 267
27X-RAY DIFFRACTION27chain 'H' and (resid 4 through 31 )H4 - 31
28X-RAY DIFFRACTION28chain 'H' and (resid 32 through 407 )H32 - 407

+
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