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- PDB-5svb: Mechanism of ATP-Dependent Acetone Carboxylation, Acetone Carboxy... -

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Basic information

Entry
Database: PDB / ID: 5svb
TitleMechanism of ATP-Dependent Acetone Carboxylation, Acetone Carboxylase AMP bound structure
Components(Acetone carboxylase ...) x 3
KeywordsLIGASE / Acetone Carboxylase / ATP / AMP / manganese / zinc / acetoacetate
Function / homology
Function and homology information


acetone carboxylase / acetone carboxylase activity / cellular detoxification of acetone / 5-oxoprolinase (ATP-hydrolyzing) activity / glutathione metabolic process / ATP binding / cytosol
Similarity search - Function
Oxoprolinase family / : / Acetophenone carboxylase beta subunit/Acetone carboxylase gamma subunit / Acetone carboxylase gamma subunit / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase, N-terminal / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase N-terminal region / Hydantoinase/oxoprolinase C-terminal domain / Hydantoinase A/oxoprolinase ...Oxoprolinase family / : / Acetophenone carboxylase beta subunit/Acetone carboxylase gamma subunit / Acetone carboxylase gamma subunit / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase, N-terminal / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase N-terminal region / Hydantoinase/oxoprolinase C-terminal domain / Hydantoinase A/oxoprolinase / Hydantoinase/oxoprolinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / Acetone carboxylase gamma subunit / Acetone carboxylase alpha subunit / Acetone carboxylase beta subunit
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.645 Å
AuthorsEilers, B.J. / Mus, F. / Alleman, A.B. / Kabasakal, B.V. / Murray, J.W. / Nocek, B.P. / Dubois, J.L. / Peters, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02- 04ER15563 United States
CitationJournal: Sci Rep / Year: 2017
Title: Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation.
Authors: Mus, F. / Eilers, B.J. / Alleman, A.B. / Kabasakal, B.V. / Wells, J.N. / Murray, J.W. / Nocek, B.P. / DuBois, J.L. / Peters, J.W.
History
DepositionAug 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetone carboxylase alpha subunit
B: Acetone carboxylase beta subunit
C: Acetone carboxylase gamma subunit
D: Acetone carboxylase alpha subunit
E: Acetone carboxylase beta subunit
F: Acetone carboxylase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,06914
Polymers376,9416
Non-polymers1,1278
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35690 Å2
ΔGint-227 kcal/mol
Surface area103890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.928, 100.209, 441.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Acetone carboxylase ... , 3 types, 6 molecules ADBECF

#1: Protein Acetone carboxylase alpha subunit


Mass: 87706.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (bacteria)
Strain: ATCC BAA-1158 / Py2 / Gene: acxB, Xaut_3510 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RM03, acetone carboxylase
#2: Protein Acetone carboxylase beta subunit


Mass: 80731.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (bacteria)
Strain: ATCC BAA-1158 / Py2 / Gene: acxA, Xaut_3509 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RM04, acetone carboxylase
#3: Protein Acetone carboxylase gamma subunit


Mass: 20033.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (bacteria)
Strain: ATCC BAA-1158 / Py2 / Gene: acxC, Xaut_3511 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RM02, acetone carboxylase

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Non-polymers , 5 types, 325 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 12-18%PEG 3350 and 0.2M MgSO4, pH and cryo was the addition of 15% glycerol
PH range: 6.3-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.645→39.623 Å / Num. obs: 115356 / % possible obs: 98.3 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.158 / Net I/σ(I): 13.2
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.567 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.645→39.623 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 5665 5.04 %
Rwork0.1978 --
obs0.1993 112445 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.645→39.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25403 0 60 317 25780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326135
X-RAY DIFFRACTIONf_angle_d0.51835431
X-RAY DIFFRACTIONf_dihedral_angle_d14.66415394
X-RAY DIFFRACTIONf_chiral_restr0.0413781
X-RAY DIFFRACTIONf_plane_restr0.0034617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6455-2.67550.33761540.28522724X-RAY DIFFRACTION76
2.6755-2.7070.33611530.28533116X-RAY DIFFRACTION83
2.707-2.740.32091540.28853136X-RAY DIFFRACTION86
2.74-2.77470.28721610.28083111X-RAY DIFFRACTION85
2.7747-2.81120.29261710.27743324X-RAY DIFFRACTION90
2.8112-2.84970.32831870.283447X-RAY DIFFRACTION94
2.8497-2.89040.3151980.283535X-RAY DIFFRACTION96
2.8904-2.93350.3061860.26483555X-RAY DIFFRACTION97
2.9335-2.97930.32362000.27143575X-RAY DIFFRACTION98
2.9793-3.02820.30122020.26333558X-RAY DIFFRACTION97
3.0282-3.08040.3081840.25563630X-RAY DIFFRACTION98
3.0804-3.13640.31091990.25783617X-RAY DIFFRACTION98
3.1364-3.19670.25781650.2653637X-RAY DIFFRACTION99
3.1967-3.26190.29072090.24993602X-RAY DIFFRACTION98
3.2619-3.33280.27432020.23083659X-RAY DIFFRACTION98
3.3328-3.41030.26981880.2173490X-RAY DIFFRACTION96
3.4103-3.49550.24751960.20943630X-RAY DIFFRACTION97
3.4955-3.58990.2452100.19883664X-RAY DIFFRACTION99
3.5899-3.69550.21732000.1873650X-RAY DIFFRACTION99
3.6955-3.81470.20911920.18313696X-RAY DIFFRACTION99
3.8147-3.95090.19342030.16853675X-RAY DIFFRACTION99
3.9509-4.10890.17111900.15523681X-RAY DIFFRACTION98
4.1089-4.29570.18721890.14723671X-RAY DIFFRACTION99
4.2957-4.52190.1851570.14263642X-RAY DIFFRACTION97
4.5219-4.80480.16192120.14263726X-RAY DIFFRACTION99
4.8048-5.1750.16281920.15213746X-RAY DIFFRACTION100
5.175-5.69440.19792000.16683764X-RAY DIFFRACTION100
5.6944-6.51530.20682070.18113736X-RAY DIFFRACTION98
6.5153-8.19660.191980.1813831X-RAY DIFFRACTION99
8.1966-39.62740.18352060.18313952X-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)
11.03610.0378-0.54631.36961.13392.4440.0948-0.08770.05130.0517-0.02770.07670.038-0.1786-0.07770.44570.0197-0.08540.4532-0.05120.518528.702440.6544268.3116
20.8815-0.1265-0.19070.82790.3850.6126-0.0184-0.0801-0.0148-0.0710.0747-0.0853-0.05830.1113-0.05060.4298-0.0113-0.01050.3291-0.06910.396424.339763.4698245.7254
31.8588-0.3130.10230.7969-0.11141.52460.13460.1803-0.23470.0599-0.17570.22380.1023-0.16960.04040.4541-0.0249-0.02080.3551-0.14830.4664-8.003714.9038238.432
43.3148-0.3850.7331.4521-0.02630.7503-0.1094-0.0452-0.0133-0.11340.0622-0.0346-0.04050.02110.0470.4558-0.0037-0.00610.295-0.06820.36274.561448.7802239.1093
50.63640.24520.2282.52930.46610.4819-0.010.02480.0904-0.2622-0.11540.4302-0.0375-0.15190.13540.36690.0219-0.04470.39-0.10750.5051-13.521746.9337240.7649
60.9529-0.62120.25240.87220.15710.8904-0.00620.0127-0.04840.252-0.00280.0160.0415-0.02590.01120.5351-0.0244-0.0310.3191-0.07760.46965.085426.272249.876
71.7783-0.3079-0.0180.3864-0.05850.60060.03220.0498-0.10830.19880.0234-0.11460.13510.1243-0.04450.5441-0.002-0.08630.3501-0.08390.530615.637914.1615250.3911
82.3691-1.1704-0.37113.48360.79271.15310.019-0.27370.17040.5552-0.14460.3756-0.0329-0.22730.13250.4645-0.04360.08990.4177-0.09440.501-16.587338.6677259.3062
92.7107-1.6539-0.68943.2347-0.26991.5366-0.1257-0.4745-0.02720.8509-0.0244-0.11240.31510.27790.15980.7374-0.03070.01520.6323-0.13360.4906-11.315739.4155270.426
100.9786-0.73470.03621.8173-0.36250.7558-0.1092-0.3587-0.4950.4230.14240.25870.2010.0372-0.04210.6642-0.05230.010.3889-0.11780.69030.54363.5106253.9905
111.89620.1788-0.84072.08130.33331.61470.1487-0.2467-0.43870.4888-0.0075-0.10860.37990.1622-0.13370.66950.0031-0.07110.363-0.0730.6737.21581.5266255.6968
121.95940.7509-0.5170.3131-0.10782.4601-0.013-0.096-0.4078-0.1202-0.00420.07590.3871-0.08160.01020.47340.0142-0.01960.3395-0.14780.573726.786737.261227.1449
130.40520.01630.36330.0348-0.19651.9894-0.00790.1454-0.2096-0.01310.2415-0.35180.30220.2881-0.19970.58630.03150.10210.4316-0.23990.630438.278945.8038216.7164
144.2807-1.1886-2.75660.92030.4752.91710.14320.27030.2878-0.25280.0129-0.3815-0.06670.2163-0.09820.5018-0.0410.07970.5318-0.18790.490143.82750.3482219.3746
151.9318-1.1993-0.01022.71660.13651.06820.15750.3641-0.2462-0.36220.0504-0.11560.11020.1354-0.20760.5559-0.07410.1070.4333-0.20.519641.067961.1299223.6852
164.12984.1912-0.39496.88790.15730.9549-0.1654-0.29540.7161-0.42860.3146-0.34420.05580.0801-0.19870.7433-0.05180.05550.35-0.03010.437223.755174.8289231.2382
171.9695-1.2991-1.32630.99920.53032.117-0.14620.29330.1816-0.29040.2813-0.2115-0.0606-0.2808-0.08150.4917-0.0772-0.00590.3657-0.11720.42226.713971.3925235.3361
182.3003-1.01430.58772.628-0.62850.32580.16270.07920.042-0.5840.1033-0.2692-0.0040.3822-0.24330.4759-0.06680.10270.4443-0.12550.400737.989662.2659230.595
192.80080.2587-2.31983.8159-3.81747.27990.1208-0.25960.2363-0.0305-0.0297-0.55940.06670.7035-0.10120.488-0.03850.03140.492-0.22930.604549.092740.5848228.0115
201.5514-0.5045-0.29761.61021.26112.0804-0.018-0.0008-0.1415-0.02940.067-0.1028-0.00720.1321-0.06160.4266-0.0157-0.0660.51030.00510.476125.323862.6257300.7477
211.10030.1066-0.00660.3170.11391.1976-0.0791-0.0641-0.0158-0.045-0.03660.0365-0.0491-0.02920.11350.39180.0213-0.06420.3862-0.05630.378420.344891.6555286.9432
221.9824-1.9788-0.85494.1167-0.76441.584-0.0869-0.25630.37470.4877-0.0356-0.3475-0.20650.47410.13950.622-0.1043-0.18010.83820.01780.478663.064189.1552331.2982
231.45230.1890.70380.81710.30160.9008-0.08070.04320.126-0.0240.0167-0.1135-0.30960.37790.07180.4135-0.0725-0.04860.54640.0090.413252.260799.4391295.8368
242.8408-1.61020.48912.1388-1.03242.6790.0312-0.14210.4750.6559-0.1548-0.5597-0.5270.51930.04570.5833-0.1149-0.13870.74380.0060.578965.611196.8723317.4599
250.1967-0.15120.65372.045-0.93782.18280.0735-0.0195-0.0538-0.0926-0.0228-0.27760.19240.1895-0.03860.43150.0149-0.05430.6310.02320.488355.315379.4703312.0971
261.73070.2839-0.40030.6056-0.19611.3996-0.0068-0.2360.00350.0674-0.002-0.00160.08360.00490.00720.42440.0192-0.09680.56280.01540.435948.127477.5672319.068
270.07190.0142-0.26012.97440.13711.74780.02060.084-0.3844-0.22-0.0873-0.08750.49450.0820.06260.5160.0465-0.02240.7791-0.04410.615565.441472.4564295.1574
280.337-0.25970.67240.816-0.54791.3122-0.0823-0.3348-0.32870.1535-0.2016-0.23250.09890.28410.30390.53730.0486-0.08670.77190.03290.556859.322870.4788334.7404
292.1556-0.7561-0.67681.393-0.00981.74970.1358-0.3718-0.2040.2638-0.0835-0.02140.1949-0.0901-0.03990.5464-0.0131-0.09310.79320.14350.50853.753566.7469337.2774
304.31960.183-4.08236.1273-1.66444.218-0.3134-0.68670.00670.4447-0.68720.1307-0.33191.06260.50940.65870.0277-0.05620.7745-0.18680.284122.0198103.973319.207
311.46132.7685-0.32418.7873-3.10322.2690.2094-0.4774-0.03551.43760.0215-0.806-0.37780.1839-0.17670.5790.0248-0.09480.6957-0.18690.574328.560898.277314.7941
322.8796-2.0582-0.00365.8338-1.80880.7802-0.2393-0.71390.12120.815-0.1089-0.1335-0.0811-0.330.37870.40490.0688-0.03940.8103-0.14560.336914.83399.2873319.5431
333.06522.37181.71597.4679-0.58952.53570.22-1.11350.98090.5267-0.15890.3754-0.22240.2349-0.09080.6037-0.0093-0.00340.7832-0.38210.64836.175109.5378315.5724
343.4876-0.3747-3.60242.6022-0.5884.68590.2227-0.52920.80080.21150.01510.5119-0.6843-0.1905-0.24810.44860.141-0.05570.7234-0.27250.60090.2335107.0388311.6621
351.23110.2628-1.88711.3529-1.74714.3201-0.1468-0.11250.09920.31220.07120.0009-0.4858-0.54980.02210.47050.1618-0.17580.6549-0.19880.54681.0235106.987299.6964
368.61.01294.15531.16161.5125.52140.15950.46810.12340.23290.0698-0.1127-0.2562-0.2777-0.19610.62290.0892-0.17150.3709-0.03220.465215.5621108.5128281.456
372.14490.6845-0.16180.9897-1.0951.69240.0691-0.05040.28490.1063-0.00680.1032-0.3832-0.2381-0.03880.43220.0686-0.10440.3916-0.12870.44138.9951102.125290.5056
383.8269-2.68710.04154.4550.23192.6013-0.1645-0.4545-0.08590.1990.22730.2798-0.0461-0.5409-0.05350.57020.06310.03770.8268-0.1110.43740.392394.2049319.2092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 280 )
2X-RAY DIFFRACTION2chain 'A' and (resid 281 through 776 )
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 87 )
4X-RAY DIFFRACTION4chain 'B' and (resid 88 through 144 )
5X-RAY DIFFRACTION5chain 'B' and (resid 145 through 275 )
6X-RAY DIFFRACTION6chain 'B' and (resid 276 through 380 )
7X-RAY DIFFRACTION7chain 'B' and (resid 381 through 496 )
8X-RAY DIFFRACTION8chain 'B' and (resid 497 through 575 )
9X-RAY DIFFRACTION9chain 'B' and (resid 576 through 629 )
10X-RAY DIFFRACTION10chain 'B' and (resid 630 through 664 )
11X-RAY DIFFRACTION11chain 'B' and (resid 665 through 717 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 42 )
13X-RAY DIFFRACTION13chain 'C' and (resid 43 through 54 )
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 74 )
15X-RAY DIFFRACTION15chain 'C' and (resid 75 through 96 )
16X-RAY DIFFRACTION16chain 'C' and (resid 97 through 106 )
17X-RAY DIFFRACTION17chain 'C' and (resid 107 through 123 )
18X-RAY DIFFRACTION18chain 'C' and (resid 124 through 149 )
19X-RAY DIFFRACTION19chain 'C' and (resid 150 through 168 )
20X-RAY DIFFRACTION20chain 'D' and (resid 14 through 280 )
21X-RAY DIFFRACTION21chain 'D' and (resid 281 through 776 )
22X-RAY DIFFRACTION22chain 'E' and (resid 8 through 69 )
23X-RAY DIFFRACTION23chain 'E' and (resid 70 through 237 )
24X-RAY DIFFRACTION24chain 'E' and (resid 238 through 275 )
25X-RAY DIFFRACTION25chain 'E' and (resid 276 through 349 )
26X-RAY DIFFRACTION26chain 'E' and (resid 350 through 556 )
27X-RAY DIFFRACTION27chain 'E' and (resid 557 through 629 )
28X-RAY DIFFRACTION28chain 'E' and (resid 630 through 664 )
29X-RAY DIFFRACTION29chain 'E' and (resid 665 through 717 )
30X-RAY DIFFRACTION30chain 'F' and (resid 2 through 13 )
31X-RAY DIFFRACTION31chain 'F' and (resid 14 through 26 )
32X-RAY DIFFRACTION32chain 'F' and (resid 27 through 42 )
33X-RAY DIFFRACTION33chain 'F' and (resid 43 through 54 )
34X-RAY DIFFRACTION34chain 'F' and (resid 55 through 74 )
35X-RAY DIFFRACTION35chain 'F' and (resid 75 through 96 )
36X-RAY DIFFRACTION36chain 'F' and (resid 97 through 106 )
37X-RAY DIFFRACTION37chain 'F' and (resid 107 through 149 )
38X-RAY DIFFRACTION38chain 'F' and (resid 150 through 166 )

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