[English] 日本語
Yorodumi
- PDB-8ih6: Crystal structure of decarboxylase-hydratase complex from Pseudom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ih6
TitleCrystal structure of decarboxylase-hydratase complex from Pseudomonas species AP-3
Components
  • 2-oxopent-4-enoate hydratase
  • 4-oxalocrotonate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / meta-cleavage pathway for 2-aminophenol catabolism. decarboxylase-hydratase complex
Function / homology
Function and homology information


2-oxo-3-hexenedioate decarboxylase / 4-oxalocrotonate decarboxylase activity / 2-oxopent-4-enoate hydratase / 2-oxopent-4-enoate hydratase activity / :
Similarity search - Function
Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family
Similarity search - Domain/homology
4-oxalocrotonate decarboxylase / 2-oxopent-4-enoate hydratase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.519 Å
AuthorsShi, Q.L. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0505903 China
CitationJournal: To Be Published
Title: Crystal structure of decarboxylase-hydratase complex from Pseudomonas species AP-3
Authors: Shi, Q.L. / Su, D.
History
DepositionFeb 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-oxopent-4-enoate hydratase
B: 2-oxopent-4-enoate hydratase
F: 4-oxalocrotonate decarboxylase
C: 2-oxopent-4-enoate hydratase
D: 2-oxopent-4-enoate hydratase
E: 2-oxopent-4-enoate hydratase
G: 4-oxalocrotonate decarboxylase
H: 4-oxalocrotonate decarboxylase
I: 4-oxalocrotonate decarboxylase
J: 4-oxalocrotonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,61514
Polymers277,24710
Non-polymers3684
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23510 Å2
ΔGint-80 kcal/mol
Surface area91090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.976, 107.792, 164.847
Angle α, β, γ (deg.)90.00, 124.46, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
2-oxopent-4-enoate hydratase / / 2-keto-4-pentenoate hydratase


Mass: 28081.004 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: amnF / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWS4, 2-oxopent-4-enoate hydratase
#2: Protein
4-oxalocrotonate decarboxylase /


Mass: 27368.311 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: amnE / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KWS3, 2-oxo-3-hexenedioate decarboxylase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
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: 54.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: potassium sodium tartrate tetrahydrate,BIS-TRIS,polyethylene glycol 6000

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.519→30.352 Å / Num. obs: 99493 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.992 / Net I/σ(I): 13
Reflection shellResolution: 2.52→2.58 Å / Num. unique obs: 7294 / CC1/2: 0.815

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.519→30.352 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 4865 4.9 %4.9%
Rwork0.1736 ---
obs0.1772 99368 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.519→30.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19084 0 24 593 19701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819412
X-RAY DIFFRACTIONf_angle_d0.96526375
X-RAY DIFFRACTIONf_dihedral_angle_d5.86911697
X-RAY DIFFRACTIONf_chiral_restr0.0523117
X-RAY DIFFRACTIONf_plane_restr0.0063466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.519-2.54770.33361750.26973137X-RAY DIFFRACTION100
2.5477-2.57760.34511680.2633119X-RAY DIFFRACTION99
2.5776-2.6090.35131760.26453113X-RAY DIFFRACTION100
2.609-2.6420.35881610.2523100X-RAY DIFFRACTION100
2.642-2.67680.34331710.2533147X-RAY DIFFRACTION100
2.6768-2.71340.29681890.2273076X-RAY DIFFRACTION100
2.7134-2.75220.31931550.22853173X-RAY DIFFRACTION100
2.7522-2.79320.33411650.20953094X-RAY DIFFRACTION100
2.7932-2.83680.34831730.21793132X-RAY DIFFRACTION100
2.8368-2.88330.29651680.22473141X-RAY DIFFRACTION100
2.8833-2.9330.30351680.21433147X-RAY DIFFRACTION100
2.933-2.98630.32311450.22753164X-RAY DIFFRACTION100
2.9863-3.04370.3051590.22113134X-RAY DIFFRACTION100
3.0437-3.10570.29031810.21783110X-RAY DIFFRACTION100
3.1057-3.17320.30331760.2163148X-RAY DIFFRACTION100
3.1732-3.24690.31111560.20373153X-RAY DIFFRACTION100
3.2469-3.3280.27911690.19153110X-RAY DIFFRACTION100
3.328-3.41790.27611630.19033170X-RAY DIFFRACTION100
3.4179-3.51830.24631630.18993152X-RAY DIFFRACTION100
3.5183-3.63170.26161450.18383153X-RAY DIFFRACTION100
3.6317-3.76130.26011720.17623140X-RAY DIFFRACTION100
3.7613-3.91160.22361650.15133167X-RAY DIFFRACTION100
3.9116-4.08920.18261520.14583183X-RAY DIFFRACTION100
4.0892-4.30420.23151380.13433187X-RAY DIFFRACTION100
4.3042-4.5730.15941460.12053173X-RAY DIFFRACTION100
4.573-4.92480.19841380.12053188X-RAY DIFFRACTION100
4.9248-5.41780.1951570.13663192X-RAY DIFFRACTION100
5.4178-6.1960.23761680.16063170X-RAY DIFFRACTION100
6.196-7.78450.20971400.15673235X-RAY DIFFRACTION100
7.7845-30.3520.19161630.14633195X-RAY DIFFRACTION98
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)
10.3180.1241-0.27250.3555-0.38870.34640.35470.16220.424-0.39-0.4060.0008-0.65520.0779-0.00090.7390.00660.18310.32040.030.6639-5.8071-33.96257.7333
21.01380.7252-1.00210.1956-0.79070.81220.15850.0110.1134-0.01260.01810.0387-0.22770.1086-00.3976-0.0050.03740.3186-0.01340.4387-11.5873-50.81614.8352
30.9855-0.02-0.66670.5890.04281.17590.0961-0.03230.02850.13630.04280.0441-0.0953-0.006400.3403-0.02250.03380.3019-0.00470.4048-15.9615-51.235322.0867
40.33350.2922-0.02740.1882-0.14580.16950.02670.3530.27580.42940.4390.04020.4908-0.25690.00190.3913-0.0077-0.05750.65770.1590.5092-38.1086-66.4669-18.4803
50.3557-0.0902-0.0880.0411-0.07920.22590.4050.43760.35250.4664-0.2598-0.20080.4963-0.6830.00090.34140.037-0.0750.76660.13620.559-48.1628-66.8124-14.6871
60.4913-0.30210.17320.2077-0.29980.40010.18970.2228-0.08280.07040.0204-0.1053-0.0533-0.08590.00010.28730.0256-0.04490.53120.07070.382-37.5347-73.5486-7.2415
70.62770.0294-0.16180.5445-0.13281.45650.05340.16050.09140.0558-0.0007-0.0005-0.0565-0.018800.24130.0093-0.04480.37940.08140.335-35.5012-70.45651.0738
80.2584-0.18650.05480.18540.16190.2719-0.07910.1462-0.01550.0204-0.02510.31330.15160.70440.00010.3808-0.0277-0.02750.50310.10320.434-30.2374-78.632416.6656
90.8974-0.2063-0.21990.6002-0.75230.8540.04890.00970.05640.04690.07160.0072-0.17260.0457-00.2983-0.0197-0.01620.34070.05440.3861-38.5182-72.24488.258
100.09610.03440.08830.0776-0.10260.0879-0.2952-1.1351-0.05221.01640.25320.1288-0.90010.340.00090.85920.0668-0.06961.0807-0.33630.7718-9.1564-50.884278.7876
110.6019-0.3534-0.62121.0249-0.01820.8901-0.0891-0.31640.07110.14780.21420.0878-0.01780.19730.00020.5325-0.00620.02630.5464-0.10520.3505-15.8427-62.631964.1398
120.2088-0.10840.06360.4886-0.0996-0.0199-0.1542-0.00730.34530.09350.3931-0.2548-0.06850.65570.00150.5422-0.0513-0.03060.753-0.260.4712-8.0213-55.639369.0234
130.48230.2910.13830.8436-0.1034-0.04530.0692-0.13390.14880.07660.05020.0231-0.04390.1543-0.00010.4621-0.02990.03180.4173-0.05830.3783-13.2235-63.419953.7484
140.4701-0.3821-0.41390.2680.27080.2380.0450.178-0.2642-0.14640.2921-0.3218-0.3054-0.25870.00060.44380.0085-0.01350.6203-0.06240.378630.8093-66.879528.8372
150.3649-0.1706-0.40680.13660.15780.7137-0.2855-0.36040.0491-0.18840.38730.2560.46530.9541-0.00660.2548-0.1509-0.24330.9025-0.1260.384630.3457-63.718739.3494
160.43930.28590.0030.3858-0.21370.0929-0.1151-0.11570.11650.20710.04640.17610.05070.2305-0.00010.3749-0.0133-0.0330.4282-0.08880.28217.9399-65.617630.8686
170.9458-0.0221-0.9452-0.1612-0.32170.4364-0.0573-0.14540.0345-0.05990.04720.020.04220.1963-00.385-0.0071-0.03090.3966-0.06040.304711.9026-72.076933.6637
180.0315-0.0482-0.0340.02110.07250.1292-0.0310.43480.0910.4401-0.16610.09180.0132-0.58860.00010.44780.0263-0.0110.5047-0.09750.5084-6.2499-73.160433.3071
190.6254-0.0528-0.2090.53170.24280.392-0.0832-0.09540.0570.05610.04740.0668-0.01690.02610.00010.3661-0.00660.00120.402-0.0320.31585.642-71.72438.7031
200.2095-0.2735-0.20290.35170.38470.50.16250.1757-0.4467-0.1412-0.1741-0.27960.37280.37970.00010.6060.1654-0.05290.47580.07820.448217.0308-118.563123.5589
210.36680.2071-0.04760.6931-0.21610.0948-0.1054-0.21680.09530.132-0.2017-0.21910.0236-0.1733-0.00010.44970.0923-0.07540.45810.01180.324311.2005-106.781126.1523
220.23430.0012-0.68160.63660.48480.7320.0011-0.0387-0.03990.022-0.0380.03360.14310.099200.41240.0526-0.03490.40480.03730.35272.0604-105.630426.7444
230.5141-0.3649-0.93870.11780.35061.5552-0.0073-0.009-0.02390.16260.0027-0.0695-0.14050.02040.00010.41790.0766-0.06290.39630.02250.3313-3.3903-101.520432.6859
240.1846-0.38450.12420.63610.10841.1403-0.40190.6785-0.07560.06640.0124-0.12860.4683-0.5462-0.00040.6184-0.1895-0.00860.5139-0.06690.5355-27.8392-118.6735-7.5989
250.6939-0.2494-0.49650.59490.49750.4562-0.22990.1788-0.17190.3825-0.03720.0698-0.0390.0612-0.00030.4641-0.04510.01550.3902-0.00050.4094-23.1316-111.74042.3702
261.04920.3463-0.34550.13121.0132.2071-0.10630.1095-0.0483-0.0346-0.03060.00440.0574-0.112700.3001-0.0216-0.0420.24780.02680.3297-27.1119-104.57686.6359
271.21030.1034-0.66320.4370.04680.90110.00280.01860.0366-0.06710.01570.0230.0622-0.01420.00010.2569-0.0007-0.03930.2630.04450.2658-28.8485-102.346115.2885
280.2612-0.1332-0.45030.21920.63042.15660.65520.17440.71850.6416-0.53830.32670.44-0.95430.07760.82280.11370.31650.40090.05040.925-57.6671-39.62350.7584
290.08260.0928-0.10090.1388-0.12790.15380.4049-0.0348-0.1412-0.3230.09650.147-0.294-0.21360.00160.8640.08630.32530.52320.00170.873-52.3282-33.099447.345
300.8438-0.7775-0.32070.88710.0140.33330.0921-0.10180.07860.2730.14090.1451-0.2255-0.0274-0.0010.52090.02380.19960.30860.04950.4425-46.9657-48.98745.3843
310.7464-0.398-0.2010.39940.36620.28140.2077-0.04650.08710.26350.00950.1642-0.19960.18310.00140.4916-0.01310.14440.28060.03030.4855-41.0495-52.479244.5576
320.4044-0.00750.30340.68260.26580.72640.1148-0.05750.09180.05280.09090.0175-0.02290.0722-0.00010.3712-0.00010.08120.29750.040.4407-36.5783-56.077139.1534
330.17750.04430.2533-0.0008-0.00260.09770.11040.4775-0.0284-0.1272-0.1659-0.0267-0.14440.08920.00010.52280.0188-0.03520.47510.05390.5289-43.5505-58.676527.8707
340.1667-0.4811-0.05231.55-0.04170.2133-0.2919-0.0853-0.52490.57270.08230.96370.0879-0.514-0.04280.2977-0.0322-0.05950.63840.22950.9314-79.3154-85.255835.4379
350.2947-0.2289-0.07251.1319-0.39120.39720.1382-0.2654-0.01930.01380.05450.6729-0.231-0.60410.07240.23940.0407-0.02160.67980.16670.7574-75.663-80.765534.9266
360.9071-0.0331-0.40550.23340.0220.1437-0.11940.00220.0631-0.18810.40470.32950.0112-0.3307-00.41280.03280.00310.48190.13930.5745-62.1118-78.284132.1325
370.6650.26920.0090.96910.10250.0158-0.0444-0.097-0.0828-0.0040.20090.086-0.1308-0.10390.00010.307-0.00810.00560.37640.12550.4275-58.7962-83.553131.6486
380.509-0.12610.23710.74690.4120.60820.03760.06240.08710.01920.14630.0561-0.1878-0.01120.00090.22410.0182-0.01620.28480.08840.3988-51.3824-80.645828.7985
390.2452-0.2988-0.12180.31430.16890.12210.1785-0.1605-0.3370.0146-0.1428-0.0480.180.0681-0.00010.24260.0158-0.0850.33130.01660.4609-49.5353-92.973523.6223
400.29480.0189-0.09370.3777-0.16680.1097-0.1108-1.11670.17220.537-0.12840.3746-0.26640.8843-0.00540.58110.0593-0.05990.70630.09850.3616-9.1644-104.478782.7071
410.3246-0.33040.04730.3092-0.05120.02550.6122-0.8193-0.60390.1021-0.6239-0.52270.22170.5907-0.01310.78210.0419-0.17420.88140.19610.6221-4.1707-111.076378.5673
420.0058-0.0928-0.05020.07550.06610.0225-0.13260.1374-0.02840.51290.33160.2667-0.23120.5752-0.0010.6540.0997-0.02760.69780.10050.4098-16.4399-103.698677.4839
430.36890.20860.19390.2365-0.08720.31880.0197-0.0470.0827-0.05090.14320.02580.49160.06620.00220.75520.12970.03220.50840.09190.4603-13.883-102.452163.2128
440.3837-0.17080.10180.11930.18170.65850.0289-0.2390.0561-0.00030.00520.19540.14340.1361-0.00010.60650.022-0.02590.49220.01190.3055-11.1178-95.762365.9415
450.2690.2979-0.07870.5115-0.35320.4215-0.1329-0.18290.03780.21620.07570.15170.10840.1136-0.00010.5830.11360.00040.47770.01090.3168-16.5705-95.131259.4624
460.6310.27740.28240.08410.08180.021-0.1303-0.3943-0.07430.11370.2892-0.08880.32180.0049-0.00040.48910.09860.01530.59720.05690.3407-6.2515-104.26269.7676
470.62450.04840.71730.55010.23350.47510.0068-0.0396-0.0550.15620.00240.0263-0.11330.091900.4490.0738-0.01380.43380.04310.3144-10.7966-94.22555.2193
480.55770.2054-0.29090.29550.04060.2795-0.5078-0.4486-0.64461.03890.395-0.09730.39890.10940.00050.9901-0.1210.32670.22110.13330.6398-50.2409-127.484750.9259
490.34310.3759-0.09280.61020.00110.2356-0.2757-0.08930.04870.38660.07490.35160.1111-0.0251-0.00130.6899-0.00640.14870.4180.05240.5552-47.4326-113.184346.7461
500.5433-0.4373-0.2230.33720.03591.138-0.1733-0.1145-0.09460.28160.08990.10840.1523-0.044800.4517-0.01120.05290.30920.07960.3811-39.3031-110.833544.6257
510.6797-0.3498-0.13860.76290.16790.0195-0.07610.00220.02160.11710.08280.01170.2267-0.0254-00.35280.0137-0.01140.2810.03940.3443-34.0783-106.498539.1292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 260 )
4X-RAY DIFFRACTION4chain 'B' and (resid -3 through 18 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 32 )
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 75 )
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 164 )
8X-RAY DIFFRACTION8chain 'B' and (resid 165 through 179 )
9X-RAY DIFFRACTION9chain 'B' and (resid 180 through 260 )
10X-RAY DIFFRACTION10chain 'F' and (resid 3 through 30 )
11X-RAY DIFFRACTION11chain 'F' and (resid 31 through 135 )
12X-RAY DIFFRACTION12chain 'F' and (resid 136 through 161 )
13X-RAY DIFFRACTION13chain 'F' and (resid 162 through 255 )
14X-RAY DIFFRACTION14chain 'C' and (resid -4 through 18 )
15X-RAY DIFFRACTION15chain 'C' and (resid 19 through 31 )
16X-RAY DIFFRACTION16chain 'C' and (resid 32 through 75 )
17X-RAY DIFFRACTION17chain 'C' and (resid 76 through 164 )
18X-RAY DIFFRACTION18chain 'C' and (resid 165 through 179 )
19X-RAY DIFFRACTION19chain 'C' and (resid 180 through 260 )
20X-RAY DIFFRACTION20chain 'D' and (resid -2 through 31 )
21X-RAY DIFFRACTION21chain 'D' and (resid 32 through 75 )
22X-RAY DIFFRACTION22chain 'D' and (resid 76 through 164 )
23X-RAY DIFFRACTION23chain 'D' and (resid 165 through 260 )
24X-RAY DIFFRACTION24chain 'E' and (resid -3 through 31 )
25X-RAY DIFFRACTION25chain 'E' and (resid 32 through 75 )
26X-RAY DIFFRACTION26chain 'E' and (resid 76 through 164 )
27X-RAY DIFFRACTION27chain 'E' and (resid 165 through 260 )
28X-RAY DIFFRACTION28chain 'G' and (resid 0 through 16 )
29X-RAY DIFFRACTION29chain 'G' and (resid 17 through 30 )
30X-RAY DIFFRACTION30chain 'G' and (resid 31 through 98 )
31X-RAY DIFFRACTION31chain 'G' and (resid 99 through 161 )
32X-RAY DIFFRACTION32chain 'G' and (resid 162 through 236 )
33X-RAY DIFFRACTION33chain 'G' and (resid 237 through 255 )
34X-RAY DIFFRACTION34chain 'H' and (resid 0 through 16 )
35X-RAY DIFFRACTION35chain 'H' and (resid 17 through 47 )
36X-RAY DIFFRACTION36chain 'H' and (resid 48 through 82 )
37X-RAY DIFFRACTION37chain 'H' and (resid 83 through 161 )
38X-RAY DIFFRACTION38chain 'H' and (resid 162 through 236 )
39X-RAY DIFFRACTION39chain 'H' and (resid 237 through 255 )
40X-RAY DIFFRACTION40chain 'I' and (resid -1 through 16 )
41X-RAY DIFFRACTION41chain 'I' and (resid 17 through 30 )
42X-RAY DIFFRACTION42chain 'I' and (resid 31 through 47 )
43X-RAY DIFFRACTION43chain 'I' and (resid 48 through 67 )
44X-RAY DIFFRACTION44chain 'I' and (resid 68 through 91 )
45X-RAY DIFFRACTION45chain 'I' and (resid 92 through 135 )
46X-RAY DIFFRACTION46chain 'I' and (resid 136 through 161 )
47X-RAY DIFFRACTION47chain 'I' and (resid 162 through 255 )
48X-RAY DIFFRACTION48chain 'J' and (resid 1 through 30 )
49X-RAY DIFFRACTION49chain 'J' and (resid 31 through 82 )
50X-RAY DIFFRACTION50chain 'J' and (resid 83 through 161 )
51X-RAY DIFFRACTION51chain 'J' and (resid 162 through 255 )

+
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