[English] 日本語
Yorodumi
- PDB-8w21: Crystal Structure of Enolase from Chlamydia trachomatis (P43212 Form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w21
TitleCrystal Structure of Enolase from Chlamydia trachomatis (P43212 Form)
ComponentsEnolase
KeywordsHYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Enolase / CHLAMYDIA TRACHOMATIS
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / cell surface / magnesium ion binding / extracellular region
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Enolase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Enolase from Chlamydia trachomatis (P43212 Form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A. / Cutter, A.P.
History
DepositionFeb 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enolase
B: Enolase
C: Enolase
D: Enolase
E: Enolase
F: Enolase
G: Enolase
H: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,59339
Polymers372,0288
Non-polymers2,56631
Water11,440635
1
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5259
Polymers93,0072
Non-polymers5187
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-41 kcal/mol
Surface area29560 Å2
MethodPISA
2
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,79811
Polymers93,0072
Non-polymers7919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-37 kcal/mol
Surface area30080 Å2
MethodPISA
3
E: Enolase
F: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6239
Polymers93,0072
Non-polymers6167
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-26 kcal/mol
Surface area29690 Å2
MethodPISA
4
G: Enolase
H: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,64810
Polymers93,0072
Non-polymers6418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-32 kcal/mol
Surface area29510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.602, 140.602, 409.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 46503.457 Da / Num. of mol.: 8 / Mutation: M78V,T178K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: D/UW-3/CX / Gene: eno, CT_587 / Plasmid: ChtrB.00084.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O84591, phosphopyruvate hydratase

-
Non-polymers , 6 types, 666 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley D7: 100 mM Potassium phosphate dibasic, 100 mM potassium chloride, 30% Peg 3350, ChtrB.00084.a.B1.PW39241 at 18.9 mg/mL. plate 13805 well D7 drop 2. Puck: PSL-0301, Cryo: 20% PEG 200 + 80% crystallant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 3, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.25→49.35 Å / Num. obs: 192780 / % possible obs: 99.3 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.054 / Rrim(I) all: 0.199 / Χ2: 1.01 / Net I/σ(I): 11.3 / Num. measured all: 2569312
Reflection shellResolution: 2.25→2.31 Å / % possible obs: 92.9 % / Redundancy: 10.3 % / Rmerge(I) obs: 1.524 / Num. measured all: 135568 / Num. unique obs: 13148 / CC1/2: 0.527 / Rpim(I) all: 0.484 / Rrim(I) all: 1.605 / Χ2: 0.98 / Net I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
PHENIXdev_5243refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→49.35 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 9522 4.94 %
Rwork0.1751 --
obs0.1773 192632 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25211 0 146 635 25992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01125834
X-RAY DIFFRACTIONf_angle_d1.13535062
X-RAY DIFFRACTIONf_dihedral_angle_d13.7949489
X-RAY DIFFRACTIONf_chiral_restr0.0594094
X-RAY DIFFRACTIONf_plane_restr0.0114620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.32362650.25995408X-RAY DIFFRACTION88
2.28-2.30.29463100.23565810X-RAY DIFFRACTION96
2.3-2.330.24713080.22325851X-RAY DIFFRACTION97
2.33-2.360.29943140.21535919X-RAY DIFFRACTION98
2.36-2.390.28043240.20866015X-RAY DIFFRACTION99
2.39-2.420.26623310.20836044X-RAY DIFFRACTION99
2.42-2.460.26572890.20836090X-RAY DIFFRACTION100
2.46-2.50.27323340.21066021X-RAY DIFFRACTION100
2.5-2.530.26563050.19766090X-RAY DIFFRACTION100
2.53-2.580.25092950.19086105X-RAY DIFFRACTION100
2.58-2.620.24473420.18316059X-RAY DIFFRACTION100
2.62-2.670.24293000.18286134X-RAY DIFFRACTION100
2.67-2.720.23783250.18456080X-RAY DIFFRACTION100
2.72-2.770.24543090.18566108X-RAY DIFFRACTION100
2.77-2.830.22813260.18646092X-RAY DIFFRACTION100
2.83-2.90.25443150.18816111X-RAY DIFFRACTION100
2.9-2.970.25533490.19976096X-RAY DIFFRACTION100
2.97-3.050.26662970.21236183X-RAY DIFFRACTION100
3.05-3.140.26973290.21566089X-RAY DIFFRACTION100
3.14-3.240.26513060.20966164X-RAY DIFFRACTION100
3.24-3.360.24773110.19756150X-RAY DIFFRACTION100
3.36-3.50.24263170.18216171X-RAY DIFFRACTION100
3.5-3.650.21073380.1736108X-RAY DIFFRACTION100
3.65-3.850.18593400.14876176X-RAY DIFFRACTION100
3.85-4.090.1743300.13386194X-RAY DIFFRACTION100
4.09-4.40.15653300.1236227X-RAY DIFFRACTION100
4.4-4.850.15193150.12136259X-RAY DIFFRACTION100
4.85-5.550.18473100.14166306X-RAY DIFFRACTION100
5.55-6.980.22163200.1756366X-RAY DIFFRACTION100
6.99-49.350.21333380.18546684X-RAY DIFFRACTION100
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)
11.14811.0555-0.12457.4048-0.95211.4763-0.0427-0.0322-0.1787-0.24170.2460.08060.0370.0155-0.19190.2371-0.0046-0.03670.31620.01280.27373.0007-27.61238.2319
21.28330.65580.33440.33410.19550.9476-0.0345-0.10970.0707-0.07540.1353-0.093-0.07110.0959-0.11080.2747-0.01780.01060.3469-0.05440.32470.7114-19.805441.6086
30.46280.8764-0.16232.85970.37720.47180.1653-0.1599-0.16320.159-0.1199-0.22810.1381-0.0017-0.00380.3067-0.039-0.03080.31530.00280.238367.8885-33.322545.7315
40.88310.36480.12531.1698-0.56721.02610.0288-0.0942-0.07780.08720.0471-0.0155-0.0632-0.0644-0.09730.24960.00430.01590.2776-0.02440.257661.064-28.936132.1066
51.6254-0.0512-0.00952.00130.70971.42350.00980.01050.1935-0.12460.0664-0.0686-0.25220.0607-0.06090.27210.01890.01810.28210.03280.286963.7595-7.012115.3934
62.14550.2257-0.4281.38150.01490.80090.0635-0.07690.36940.0524-0.00720.1239-0.145-0.0932-0.07280.33760.05380.00310.27040.01350.366152.7957-1.421.6038
72.1013-0.2270.38521.5748-0.05141.83990.0602-0.07370.05790.1446-0.0630.2916-0.0417-0.1560.00340.2769-0.00290.0260.2925-0.02850.293351.3871-18.771330.1792
82.73330.9547-0.00071.79460.88861.4631-0.00860.14980.00840.05950.01230.021-0.0797-0.0014-0.01770.24930.01770.01260.260.01140.251761.3475-22.604218.0844
91.0814-0.37230.74720.4773-0.14351.35460.13760.2131-0.0785-0.0191-0.01970.00140.10220.117-0.1120.26390.0512-0.00860.3545-0.02990.255985.9305-28.413412.9968
101.3775-0.08650.47680.9441-0.14370.832-0.03080.24260.3218-0.0705-0.0485-0.1493-0.15350.21070.06930.2481-0.02760.00840.2950.03940.327694.157-8.133426.9093
117.3734-2.2292-1.5021.89410.72721.89730.2519-0.1170.1549-0.0101-0.00690.0509-0.0564-0.1603-0.22820.36960.00230.02720.2960.02310.274538.2123-10.659984.2276
121.6577-0.58010.7281.4283-0.23971.2572-0.0396-0.06480.03180.27880.038-0.0038-0.1964-0.041-0.00420.41550.04220.02650.2928-0.02040.274740.9643-3.796389.7852
130.3698-0.1592-0.16140.7146-0.13310.9333-0.01750.00740.02550.02930.0116-0.0707-0.07350.0907-0.00110.2844-0.0213-0.01360.2836-0.00810.294351.8248-3.791866.0179
141.50630.18830.67652.5720.99312.022-0.10420.08860.32510.03440.1844-0.3305-0.21440.2778-0.06380.263-0.03020.02130.30170.02280.411766.43038.898367.1273
151.4071-0.22290.05651.755-0.12241.0924-0.0795-0.02810.26820.12380.0044-0.223-0.3530.01020.06890.3839-0.003-0.02750.2948-0.00690.317248.78227.371873.7007
161.8616-0.53981.82312.45110.54392.37630.03620.04080.137-0.2163-0.1355-0.0182-0.02390.01630.07290.25320.01550.06930.30120.00990.268943.64650.202160.9588
176.31.84070.35081.73390.06271.02560.0047-0.08520.0959-0.05750.04620.12410.0103-0.0571-0.05730.2956-0.00220.01610.28840.01190.265636.0763-17.439359.3781
182.4140.4693-0.84960.7614-0.30051.26580.040.1203-0.0285-0.0961-0.01490.03590.0527-0.0178-0.02880.3122-0.03040.00310.2638-0.00790.275541.9854-20.839553.1944
191.02650.23410.54320.8503-0.15671.1868-0.05080.0785-0.0119-0.07930.05460.08670.0611-0.14470.01130.2784-0.05290.0260.3029-0.02640.294131.0607-29.059163.0967
201.9565-0.0092-0.8591.7344-0.02991.91580.05380.0880.0781-0.01640.0448-0.1447-0.05510.1295-0.11240.28550.0057-0.00650.32180.00010.325659.5296-26.586678.7815
210.88470.0508-0.22661.6236-0.05441.478-0.0077-0.0568-0.0755-0.094-0.0619-0.27350.15660.25610.04430.24740.02360.00280.36430.01410.341466.1924-34.904674.0013
222.579-0.7834-0.80214.329-0.10185.4524-0.26690.3285-0.2496-0.4016-0.046-0.0820.8909-0.07520.27160.3808-0.0310.06630.3051-0.00010.382659.399-45.858768.7707
231.5827-1.15290.0462.93-0.76161.13360.17990.3995-0.2767-0.535-0.2629-0.22110.33690.12770.05280.3871-0.03030.04240.3372-0.06240.402748.8434-42.581765.7576
241.7380.7492-0.14850.7223-0.46281.2628-0.0879-0.0495-0.2004-0.070.0599-0.21480.0952-0.05890.030.25560.00620.01390.2636-0.03140.26443.1147-32.730370.4551
251.58810.5135-1.12362.194-0.12892.47810.0171-0.0168-0.15450.1083-0.1976-0.040.06890.12140.16140.2128-0.0086-0.00320.2446-0.01970.25543.3319-29.355381.709
261.30611.03550.31281.8920.41971.2218-0.05290.2099-0.1368-0.27860.1332-0.11570.021-0.071-0.09120.3805-0.02990.00270.3579-0.04340.2654118.0723-4.321358.8743
271.0940.3797-0.13081.23920.22590.5473-0.10190.13390.2386-0.18360.04630.3114-0.1602-0.14180.04810.28680.0257-0.08860.29970.00860.3404101.382910.438175.5028
283.26630.17371.86121.4042-1.1682.2593-0.12020.02890.34460.14190.0339-0.0939-0.1587-0.13180.07580.26040.01410.00180.2856-0.02760.273113.7686.263183.7296
291.4946-0.8012-0.31061.55330.95931.6444-0.02280.02160.02280.15910.0152-0.00610.0186-0.05970.02060.3660.0042-0.04730.2464-0.02120.2723115.0572-12.594792.5088
300.7-0.04090.02511.02610.37740.8081-0.07610.032-0.04940.1025-0.00520.16190.1192-0.16940.08330.3008-0.0220.01250.3222-0.04070.3018104.4571-22.782777.3633
313.0223-0.2014-1.37393.1018-0.26152.99070.0468-0.2785-0.230.68440.03760.69550.058-0.2408-0.04420.4471-0.08860.1620.4578-0.0960.5787.6761-36.941284.5897
321.1235-0.3234-0.2431.66780.35271.1388-0.1231-0.0713-0.2150.28450.01610.22120.2284-0.220.09580.3042-0.04080.02440.2666-0.02990.2951108.1232-29.638878.7296
331.9991-0.3952-0.34341.60220.11872.17110.03580.13780.01280.0842-0.0272-0.05610.0590.12370.00070.2470.00370.01470.3083-0.00840.263276.146148.646516.1471
343.0997-1.9907-0.2172.65060.33031.41850.19320.38170.034-0.308-0.11080.0644-0.1814-0.0444-0.07210.3278-0.00890.04810.3080.0220.249876.19265210.3881
351.0964-0.3018-0.72920.9404-0.26411.21050.11340.07470.1458-0.0886-0.0149-0.04980.008-0.0924-0.08980.27750.02180.01660.29390.01180.298965.316454.232520.9599
362.0840.04680.44471.73650.58621.72760.0894-0.127-0.37450.1476-0.036-0.14190.24220.0644-0.03350.3741-0.02060.01220.29050.03640.37168.445130.217338.8887
371.50041.0367-0.67491.1088-0.00110.8917-0.0968-0.1608-0.5781-0.04970.0025-0.05280.41170.00510.07240.42340.03320.01870.34160.11310.509970.596922.286838.9648
381.860.05120.64871.28420.60961.46950.13870.1008-0.3774-0.0561-0.08090.08290.1409-0.1728-0.06730.3478-0.0429-0.00820.2534-0.00280.423654.380224.006428.9164
391.5322-0.0615-0.03780.8137-0.00410.960.09180.1414-0.1104-0.0076-0.05240.12460.0726-0.0573-0.03370.34350.01470.02120.30650.01040.350958.802141.375625.2815
401.8445-0.65290.5142.26831.58852.068-0.0162-0.2074-0.12990.1408-0.09210.07050.0882-0.03640.10220.3163-0.01530.04150.26760.02470.269463.881346.21539.1736
411.17270.3572-0.60540.74870.02471.40550.1145-0.31870.16750.1106-0.05990.0643-0.02910.1413-0.05390.2839-0.02920.00970.3393-0.04440.268187.417854.225744.7879
421.94310.52440.1181.5215-0.34871.63990.0632-0.2418-0.36170.1619-0.0755-0.16520.31110.1531-0.01220.37130.047-0.01790.27920.03260.363299.69427.181830.5952
432.47480.2846-0.22510.9819-0.11431.2272-0.0399-0.4283-0.10850.2037-0.0326-0.17030.0880.16820.0670.3055-0.0044-0.01680.33060.00530.289699.993344.95833.7214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 153 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 371 )
8X-RAY DIFFRACTION8chain 'A' and (resid 372 through 423 )
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 147 )
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 423 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 29 )
12X-RAY DIFFRACTION12chain 'C' and (resid 30 through 109 )
13X-RAY DIFFRACTION13chain 'C' and (resid 110 through 216 )
14X-RAY DIFFRACTION14chain 'C' and (resid 217 through 301 )
15X-RAY DIFFRACTION15chain 'C' and (resid 302 through 392 )
16X-RAY DIFFRACTION16chain 'C' and (resid 393 through 424 )
17X-RAY DIFFRACTION17chain 'D' and (resid 3 through 29 )
18X-RAY DIFFRACTION18chain 'D' and (resid 30 through 75 )
19X-RAY DIFFRACTION19chain 'D' and (resid 76 through 147 )
20X-RAY DIFFRACTION20chain 'D' and (resid 148 through 197 )
21X-RAY DIFFRACTION21chain 'D' and (resid 198 through 276 )
22X-RAY DIFFRACTION22chain 'D' and (resid 277 through 301 )
23X-RAY DIFFRACTION23chain 'D' and (resid 302 through 341 )
24X-RAY DIFFRACTION24chain 'D' and (resid 342 through 392 )
25X-RAY DIFFRACTION25chain 'D' and (resid 393 through 424 )
26X-RAY DIFFRACTION26chain 'E' and (resid 3 through 128 )
27X-RAY DIFFRACTION27chain 'E' and (resid 129 through 392 )
28X-RAY DIFFRACTION28chain 'E' and (resid 393 through 424 )
29X-RAY DIFFRACTION29chain 'F' and (resid 3 through 75 )
30X-RAY DIFFRACTION30chain 'F' and (resid 76 through 250 )
31X-RAY DIFFRACTION31chain 'F' and (resid 251 through 301 )
32X-RAY DIFFRACTION32chain 'F' and (resid 302 through 424 )
33X-RAY DIFFRACTION33chain 'G' and (resid 3 through 58 )
34X-RAY DIFFRACTION34chain 'G' and (resid 59 through 88 )
35X-RAY DIFFRACTION35chain 'G' and (resid 89 through 147 )
36X-RAY DIFFRACTION36chain 'G' and (resid 148 through 197 )
37X-RAY DIFFRACTION37chain 'G' and (resid 198 through 230 )
38X-RAY DIFFRACTION38chain 'G' and (resid 231 through 301 )
39X-RAY DIFFRACTION39chain 'G' and (resid 302 through 392 )
40X-RAY DIFFRACTION40chain 'G' and (resid 393 through 424 )
41X-RAY DIFFRACTION41chain 'H' and (resid 3 through 147 )
42X-RAY DIFFRACTION42chain 'H' and (resid 148 through 301 )
43X-RAY DIFFRACTION43chain 'H' and (resid 302 through 424 )

+
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