[English] 日本語
Yorodumi
- PDB-4du6: Crystal structure of GTP cyclohydrolase I from Yersinia pestis co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4du6
TitleCrystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP
ComponentsGTP cyclohydrolase 1
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold
Function / homology
Function and homology information


: / GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / zinc ion binding / cytoplasm
Similarity search - Function
GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 ...GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / GTP cyclohydrolase 1 / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.106 Å
AuthorsMaltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Source and taxonomy
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,96224
Polymers125,1095
Non-polymers3,85319
Water3,279182
1
A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
hetero molecules

A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,92448
Polymers250,21710
Non-polymers7,70738
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area69500 Å2
ΔGint-228 kcal/mol
Surface area67680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.047, 104.912, 70.070
Angle α, β, γ (deg.)90.00, 96.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-404-

HOH

Details-x+1,y,-z is applied to the asymmetric unit (pentamer) to generate decamer.

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
GTP cyclohydrolase 1 / GTP cyclohydrolase I


Mass: 25021.715 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: folE, YPTB1520 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q66C86, UniProt: Q8ZG15*PLUS, GTP cyclohydrolase I

-
Non-polymers , 6 types, 201 molecules

#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M Lithium Chloride; 0.1M TRIS HCl pH 8.5; 8% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.106→50 Å / Num. all: 70010 / Num. obs: 70010 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 37.55 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2881 / Rsym value: 0.482 / % possible all: 80.9

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GTP

1gtp


Resolution: 2.106→43.198 Å / SU ML: 0.27 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3519 5.05 %random
Rwork0.18 ---
all0.182 69649 --
obs0.182 69649 96.32 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.745 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 57.1 Å2
Baniso -1Baniso -2Baniso -3
1--17.3027 Å2-0 Å2-1.0167 Å2
2---5.871 Å20 Å2
3---23.1737 Å2
Refinement stepCycle: LAST / Resolution: 2.106→43.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8535 0 236 182 8953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139122
X-RAY DIFFRACTIONf_angle_d1.48212398
X-RAY DIFFRACTIONf_dihedral_angle_d183475
X-RAY DIFFRACTIONf_chiral_restr0.1011476
X-RAY DIFFRACTIONf_plane_restr0.0061563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1058-2.13470.341930.28182004209772
2.1347-2.16510.32141100.25412283239384
2.1651-2.19750.2531390.24722295243485
2.1975-2.23180.31361380.24192397253588
2.2318-2.26840.31741410.23442550269193
2.2684-2.30750.30771490.22912629277896
2.3075-2.34950.25751580.22352676283499
2.3495-2.39460.26631460.20292705285199
2.3946-2.44350.25571450.21692720286599
2.4435-2.49660.25511440.21532724286899
2.4966-2.55470.28071330.21252699283299
2.5547-2.61860.24391520.20852688284099
2.6186-2.68940.29091700.20862746291699
2.6894-2.76850.29341360.206626892825100
2.7685-2.85780.27651290.20292756288599
2.8578-2.960.26861450.227172862100
2.96-3.07850.22041330.200327812914100
3.0785-3.21850.27641500.18927132863100
3.2185-3.38810.23361230.18327752898100
3.3881-3.60030.23751420.171227392881100
3.6003-3.87810.21371450.167227492894100
3.8781-4.26810.19191500.141727552905100
4.2681-4.8850.15851540.129227572911100
4.885-6.15170.20941480.174427742922100
6.1517-43.20680.1691460.16232809295599
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)
14.633-1.0917-1.78447.9198-1.71045.76630.0610.54630.068-0.585-0.1649-1.4159-0.04931.0472-0.00050.3599-0.10550.14590.8141-0.03620.6108127.9851-6.0771-18.0341
23.15311.48012.96132.33661.5923.1014-0.16610.1214-0.191-0.18320.2281-0.2613-0.23260.819-0.03480.4024-0.1467-0.07220.64120.10560.7401132.36788.05770.9285
32.6018-1.6763-1.32191.54020.10951.8761-0.0934-1.1435-0.32090.4524-0.0186-0.25890.13060.21260.05880.6035-0.1421-0.24790.79890.05440.6583124.583712.025519.779
41.57452.48082.01157.1148.29912.0946-0.0963-0.0091-0.08710.3928-0.1565-0.07470.52350.39940.37960.3996-0.027900.52680.09620.6068125.92151.22191.8644
53.36451.81371.34134.95281.872.6528-0.04720.1957-0.1495-0.10570.0457-0.20970.07360.27450.02510.2427-0.04020.06410.42220.02690.3208112.8894-6.32-11.9459
61.0998-0.847-0.29912.04361.68132.196-0.03670.18640.2487-0.16390.0497-0.2043-0.16490.18820.01350.3115-0.08950.05150.40370.05810.4163110.35024.0653-14.1244
72.07631.1180.12622.09242.77552.02390.0262-0.09661.23220.4485-0.38610.878-0.0591-1.04510.46630.5187-0.03450.06850.5797-0.0720.670798.5316-1.4772-20.5495
86.63822.3508-1.2333.4134-2.34726.7882-0.02460.4705-1.1398-0.6549-0.0506-0.08060.84610.4418-0.05770.53610.05860.04130.4771-0.24470.629695.1638-38.3096-21.707
92.3526-1.38212.52019.534-6.77882.02530.60490.48110.0094-0.7333-0.8239-0.83081.44010.36550.1450.79030.09570.10790.702-0.19460.8437105.9894-40.1717-13.7336
105.70332.29795.25064.39651.33828.7445-0.12020.1546-0.44120.30620.00370.2020.93990.52530.07730.42640.14720.06530.3734-0.0010.6254109.661-40.39295.0066
113.89991.76832.73574.80050.05065.61790.2859-0.7752-0.52530.7458-0.06650.04180.208-0.0782-0.22410.46620.1308-0.01140.55510.05110.5194109.5793-33.133217.3189
124.896-0.75356.80940.62370.15142.04780.159-0.1901-0.42810.05290.0255-0.00730.7426-0.384-0.11390.3924-0.00250.06810.3031-0.01870.544499.8712-36.1488-1.0458
137.8163-0.88144.02132.9188-1.13844.79390.26460.2829-0.8736-0.67860.31981.0670.7124-0.7687-0.60180.436-0.1029-0.02510.6109-0.08210.551578.6741-27.0369-22.5488
147.2866-1.44164.08651.287-1.23264.6910.01210.111-0.4726-0.06230.1593-0.02390.1635-0.1198-0.17580.2855-0.02850.06950.2557-0.0240.322393.2211-21.9539-12.3919
152.36750.22731.28680.9220.30772.44530.00690.2361-0.2481-0.10910.0147-0.05690.1750.256-0.0270.2866-0.00850.08290.2888-0.03490.344297.3929-21.1806-14.4301
162.0345-1.3564-0.56947.4485-1.28578.59690.0335-0.06091.57770.3853-0.3833-0.2383-1.1417-0.10450.37040.3586-0.05430.00430.491-0.10120.559890.1678-8.7744-23.6535
172.0186-5.3303-4.72787.51923.28937.08270.09661.6026-0.9701-0.1574-0.65081.48970.6109-1.87610.53010.4698-0.0996-0.11120.8946-0.17850.72554.5687-16.7978-26.3002
182.00065.6354-9.10694.3306-5.95188.4385-1.18390.6602-1.6097-0.54180.2947-0.63151.16-1.45230.81070.5593-0.2058-0.02360.9058-0.02020.79256.0285-28.0887-19.4852
195.1118-2.77773.68223.6452-1.30484.63030.1156-0.3788-0.14880.1421-0.11060.61510.3475-0.5485-0.01280.3477-0.15120.05360.46260.01570.521855.2642-34.1857-1.037
205.7679-2.12081.0684.40050.03154.3717-0.4219-1.0956-0.31970.53680.4520.95650.4137-0.56810.0680.4125-0.06150.09980.58460.10980.593461.0026-32.998911.8033
211.7669-1.16192.26673.1974-3.34997.4883-0.18070.05-0.0434-0.0373-0.01140.20450.1416-1.01050.18960.28-0.06040.0050.524-0.05480.528756.5783-22.6974-5.8899
222.86050.63230.05366.0474-2.02453.0344-0.07870.37030.2595-0.23790.05970.5303-0.2081-0.43570.03290.25340.0155-0.02450.4209-0.03250.361264.8591-7.7545-17.6219
233.755-2.24914.31553.6289-4.59858.2480.06630.2905-0.2634-0.25460.0340.18970.14530.0823-0.09420.2241-0.00520.01540.2877-0.0780.290373.622-14.8986-18.3122
242.04051.21050.6182.0571.41382.0179-0.2807-0.04560.54540.4988-0.1742-0.877-0.22911.09790.5440.52250.0321-0.12510.50690.06330.582281.2144-2.6551-23.067
254.3714-0.78260.1828.59662.10734.67480.10210.49991.18640.0023-0.09620.0305-0.8316-0.733-0.07180.87610.2399-0.13870.68160.19650.826662.176928.7256-25.3575
269.6016-8.4028-9.34069.4627.29469.37770.54141.59670.70530.0157-0.78880.788-0.6553-1.46330.21630.62940.1617-0.08580.8258-0.02460.866751.013923.3408-19.3723
275.19070.0665-3.18120.72660.23212.91070.1140.02460.6107-0.1166-0.04960.1793-0.4853-0.1194-0.05590.44050.0998-0.14250.39660.01790.555561.84320.0455-8.8304
281.4810.4826-0.20841.8978-1.05821.7825-0.11850.2430.3982-0.08650.15670.1943-0.2885-0.2681-0.02650.44760.0781-0.10520.42980.04240.455869.085113.0969-17.6119
292.02291.7653-0.45549.497-3.44369.9622-0.3854-0.1286-1.41680.5171-0.5092-1.01670.57650.99710.9130.4367-0.02070.00580.4540.16240.702283.93388.1386-23.9703
302.83420.7014-0.17933.00581.29453.92490.00610.04860.9812-0.6967-0.0358-0.4463-1.50470.34180.07351.1446-0.1893-0.02740.55110.26041.0771104.467737.8388-18.3922
312.6325-0.0782-1.01123.71950.26791.562-0.16530.08840.2578-0.1968-0.19530.0783-0.62010.12520.20561.8703-0.0918-0.04750.4066-0.08781.275892.120547.29612.9955
326.6574-0.4905-0.4433.3561-1.40724.48120.4988-0.97131.36140.16480.0257-0.2143-1.47950.1959-0.50021.1665-0.045-0.03020.6452-0.26340.950385.550342.148414.6542
333.8063-1.6917-3.50511.57230.07465.7610.1991-0.4581.17280.00020.0143-0.4637-1.40410.9287-0.2010.972-0.2632-0.08270.4716-0.03940.950298.772437.501-1.1969
343.0163-1.1111-1.31697.41454.22114.9441-0.09670.20450.3157-0.04070.7627-1.3134-0.31150.9555-0.75280.5161-0.1970.01550.6797-0.00690.6372114.337916.5913-18.3893
354.3172-2.1324-2.45624.0432.06163.86610.10640.13020.3889-0.04890.0481-0.0779-0.46810.1503-0.10360.4396-0.1059-0.02070.32460.08230.462797.908921.5854-11.9422
362.1801-0.0563-0.34452.06140.82271.9744-0.05780.09870.4777-0.2142-0.129-0.4354-0.63910.31970.2040.5908-0.1411-0.0380.36220.13760.6347100.57626.165-14.1894
379.2258-3.348-7.88092.96653.34258.68310.09380.59710.4479-0.0731-0.1565-0.2019-0.6201-0.30270.08370.4273-0.0351-0.08770.31910.11520.480691.690521.6998-13.5165
389.8195-1.0016-7.41952.04240.52077.02170.25070.34940.8533-0.21850.0885-0.1379-0.5943-0.1624-0.33380.5083-0.0569-0.10930.33240.08640.475887.1119.6325-15.73
399.60330.3964-4.77372.0399-1.33332.0178-0.33040.2559-1.39490.2138-0.47360.54430.7245-0.48860.88490.4951-0.070.0920.55860.01190.623394.94277.8909-22.7284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:18)
2X-RAY DIFFRACTION2chain 'A' and (resseq 19:49)
3X-RAY DIFFRACTION3chain 'A' and (resseq 50:60)
4X-RAY DIFFRACTION4chain 'A' and (resseq 61:81)
5X-RAY DIFFRACTION5chain 'A' and (resseq 82:149)
6X-RAY DIFFRACTION6chain 'A' and (resseq 150:205)
7X-RAY DIFFRACTION7chain 'A' and (resseq 206:220)
8X-RAY DIFFRACTION8chain 'B' and (resseq 2:18)
9X-RAY DIFFRACTION9chain 'B' and (resseq 19:30)
10X-RAY DIFFRACTION10chain 'B' and (resseq 31:48)
11X-RAY DIFFRACTION11chain 'B' and (resseq 49:60)
12X-RAY DIFFRACTION12chain 'B' and (resseq 61:81)
13X-RAY DIFFRACTION13chain 'B' and (resseq 82:97)
14X-RAY DIFFRACTION14chain 'B' and (resseq 98:132)
15X-RAY DIFFRACTION15chain 'B' and (resseq 133:205)
16X-RAY DIFFRACTION16chain 'B' and (resseq 206:217)
17X-RAY DIFFRACTION17chain 'C' and (resseq 2:18)
18X-RAY DIFFRACTION18chain 'C' and (resseq 19:30)
19X-RAY DIFFRACTION19chain 'C' and (resseq 31:48)
20X-RAY DIFFRACTION20chain 'C' and (resseq 49:60)
21X-RAY DIFFRACTION21chain 'C' and (resseq 61:81)
22X-RAY DIFFRACTION22chain 'C' and (resseq 82:149)
23X-RAY DIFFRACTION23chain 'C' and (resseq 150:205)
24X-RAY DIFFRACTION24chain 'C' and (resseq 206:220)
25X-RAY DIFFRACTION25chain 'D' and (resseq 2:18)
26X-RAY DIFFRACTION26chain 'D' and (resseq 19:30)
27X-RAY DIFFRACTION27chain 'D' and (resseq 31:132)
28X-RAY DIFFRACTION28chain 'D' and (resseq 133:205)
29X-RAY DIFFRACTION29chain 'D' and (resseq 206:217)
30X-RAY DIFFRACTION30chain 'E' and (resseq 2:30)
31X-RAY DIFFRACTION31chain 'E' and (resseq 31:48)
32X-RAY DIFFRACTION32chain 'E' and (resseq 49:60)
33X-RAY DIFFRACTION33chain 'E' and (resseq 61:81)
34X-RAY DIFFRACTION34chain 'E' and (resseq 82:97)
35X-RAY DIFFRACTION35chain 'E' and (resseq 98:132)
36X-RAY DIFFRACTION36chain 'E' and (resseq 133:165)
37X-RAY DIFFRACTION37chain 'E' and (resseq 166:182)
38X-RAY DIFFRACTION38chain 'E' and (resseq 183:205)
39X-RAY DIFFRACTION39chain 'E' and (resseq 206:218)

+
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