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- PDB-5hw2: Crystal Structure of Adenylosuccinate Lyase from Francisella tula... -

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Basic information

Entry
Database: PDB / ID: 5hw2
TitleCrystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with fumaric acid
ComponentsAdenylosuccinate lyase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / nucleotide binding
Similarity search - Function
Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) ...Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FUMARIC ACID / : / PHOSPHATE ION / Adenylosuccinate lyase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsChang, C. / Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with fumaric acid
Authors: Chang, C. / Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
C: Adenylosuccinate lyase
D: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,92920
Polymers200,7344
Non-polymers1,19516
Water17,835990
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29250 Å2
ΔGint-111 kcal/mol
Surface area59390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.680, 88.680, 255.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Adenylosuccinate lyase


Mass: 50183.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: purB, FTT_0015, BZ14_879 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5NIQ1, adenylosuccinate lyase

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Non-polymers , 5 types, 1006 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: K
#3: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H4O4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 1.5 M Sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979206 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979206 Å / Relative weight: 1
Reflection twinOperator: -h,k,-l / Fraction: 0.49
ReflectionResolution: 2.05→50 Å / Num. obs: 120165 / % possible obs: 98.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Χ2: 1.119 / Net I/av σ(I): 15.892 / Net I/σ(I): 8.5 / Num. measured all: 683828
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.095.50.61759990.8150.2760.6790.69898.6
2.09-2.125.60.53660570.8310.2390.590.7199.3
2.12-2.165.60.45860350.8990.2030.5040.75799.3
2.16-2.215.70.39960270.9050.1750.4380.81399.2
2.21-2.265.70.34960450.9140.1520.3830.86999.2
2.26-2.315.70.30260340.9380.1310.3310.94498.9
2.31-2.375.80.27960100.9470.1190.3050.98499
2.37-2.435.80.24260250.9570.1030.2641.05299.2
2.43-2.55.80.2260430.9580.0930.241.1398.6
2.5-2.585.80.19259980.9690.0810.2091.22498.8
2.58-2.685.80.18260080.9620.0770.1991.30298.4
2.68-2.785.70.15659850.9740.0660.171.36798.1
2.78-2.915.70.13859460.9730.0590.1511.41397.9
2.91-3.065.60.11759420.9790.0510.1281.597.9
3.06-3.255.50.09959600.9840.0430.1081.56197.7
3.25-3.515.40.08459580.9860.0370.0931.56397.4
3.51-3.865.30.07859440.9880.0340.0861.59897.5
3.86-4.425.30.06759700.9880.030.0741.40197.8
4.42-5.565.50.05660310.9880.0250.0611.06298.4
5.56-507.10.04161480.9980.0160.0440.69499.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
MOLREPphasing
SBC-Collectdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EEI
Resolution: 2.054→36.432 Å / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 26.73 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2452 11829 5.23 %
Rwork0.1882 214694 -
obs0.1919 113636 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.88 Å2 / Biso mean: 35.8537 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.054→36.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13276 0 68 990 14334
Biso mean--31.3 27.09 -
Num. residues----1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813573
X-RAY DIFFRACTIONf_angle_d0.49818271
X-RAY DIFFRACTIONf_chiral_restr0.0452077
X-RAY DIFFRACTIONf_plane_restr0.0042338
X-RAY DIFFRACTIONf_dihedral_angle_d13.8848289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0553-2.09070.33713880.27148509889770
2.0907-2.12870.29214320.2679087951975
2.1287-2.16960.3514700.26359475994578
2.1696-2.21390.30365240.255497061023080
2.2139-2.2620.30346250.256199451057082
2.262-2.31460.28386210.2389102971091885
2.3146-2.37240.27695510.2416109451149691
2.3724-2.43650.29065600.2313112521181293
2.4365-2.50820.28395840.2233113101189493
2.5082-2.5890.28336340.2185112411187594
2.589-2.68150.28516100.2214113991200993
2.6815-2.78870.27146400.2125112611190193
2.7887-2.91550.27485820.209113041188693
2.9155-3.0690.26435460.1966112761182293
3.069-3.26090.2826160.1852112791189593
3.2609-3.51210.2416460.1668111681181492
3.5121-3.86450.21166120.1492112101182293
3.8645-4.42130.17755870.1334112661185393
4.4213-5.56130.18196440.1354113121195693
5.5613-25.87790.19766250.1636114521207795
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)
10.69050.08860.12110.65110.22720.6005-0.1482-0.01270.2759-0.31170.0789-0.1289-0.35230.10760.03060.3884-0.08290.0690.1176-0.00260.2491-10.04080.047-0.2294
20.6163-0.18250.01260.7229-0.21930.5450.0636-0.0765-0.044-0.1495-0.08330.21050.0377-0.1074-0.01280.17650.0024-0.02380.2321-0.02590.1089-38.4441-26.6782-2.4978
30.007-0.0604-0.00350.54750.06720.0282-0.0514-0.14210.1494-0.1431-0.04360.0437-0.0502-0.00420.07640.3183-0.02170.00560.2097-0.05390.2603-13.40144.014216.6479
40.62260.29050.12090.92770.07810.5404-0.061-0.04590.0394-0.22590.04670.017-0.0752-0.0709-0.02280.1836-0.0042-0.00720.10320.00390.1077-23.7885-17.57421.2401
50.1577-0.0223-0.02750.16520.06840.21840.0093-0.03760.0339-0.12920.0118-0.00710.01530.028-0.02670.2139-0.0350.04060.092-0.00970.1302-16.2009-19.32671.8792
61.24660.3739-0.23190.64340.16220.1613-0.0045-0.0267-0.4603-0.3503-0.06360.24720.269-0.13210.08630.4369-0.1783-0.15910.4390.03140.4905-53.5625-46.3922-4.0336
70.00790.08060.03171.8166-1.39411.71350.02520.02170.04660.06170.00570.2833-0.1046-0.2902-0.06920.6766-0.186-0.29980.5890.04470.5894-66.9636-50.1047-4.056
80.5499-0.2697-0.0250.7716-0.55830.45780.1685-0.0033-0.0346-0.08420.18240.3149-0.0462-0.09580.00360.3085-0.054-0.28910.3096-0.07420.2227-52.1381-24.3103-5.8157
91.64860.52740.82080.36910.32010.7976-0.1438-0.0428-0.10530.0034-0.05230.30590.08070.02430.05130.1769-0.01160.04060.53720.06780.1954-41.9736-33.729725.0742
100.4407-0.355-0.24731.9112-0.31870.30210.03490.03330.0570.1173-0.09460.1087-0.1128-0.04620.0090.2968-0.04920.05510.58260.11930.4804-59.3169-38.098422.1711
110.03880.111-0.00520.4122-0.41041.21030.0507-0.1609-0.2535-0.04130.020.13830.2620.0720.00120.2907-0.1619-0.03540.52250.19270.4981-49.6578-46.561319.4133
120.54350.15250.02290.78920.11760.327-0.0424-0.21250.0427-0.05040.02910.0556-0.1165-0.1293-0.02530.1169-0.00030.01480.2722-0.02260.1181-27.8251-17.338122.132
130.4372-0.1252-0.26180.6351-0.12940.59390.0149-0.1855-0.0366-0.02520.0283-0.0268-0.0316-0.1452-0.0020.05680.00120.02480.20790.03850.1079-25.0775-28.436420.6149
140.14380.0628-0.11170.5807-0.40510.3965-0.0379-0.06830.206-0.17270.1674-0.232-0.07350.0646-0.04440.2652-0.055-0.04620.6298-0.27580.3735-2.42993.791631.8391
150.3628-0.24320.21030.2655-0.14410.1252-0.0129-0.03270.0584-0.0133-0.0580.0229-0.0145-0.0390.01650.6455-0.2030.03690.5563-0.18530.95748.523819.122321.9356
160.83490.2685-0.03420.25150.15210.19820.03640.02380.2471-0.0491-0.0112-0.1307-0.27190.0508-0.01590.3354-0.0237-0.01370.2175-0.1130.3189-10.202912.283428.1351
170.033-0.08910.28260.3543-0.08390.8113-0.0921-0.0567-0.03830.03670.0879-0.09090.10670.14360.04560.2843-0.04480.02910.48750.15370.2043-10.2279-47.899139.4759
180.59090.4493-0.1530.7806-0.01140.6981-0.0768-0.09210.02070.21490.0637-0.0687-0.08860.00170.0040.19630.0019-0.00830.44040.1270.2013-9.8038-38.581248.7763
190.36350.06930.43630.12840.22261.2683-0.184-0.092-0.3514-0.05050.108-0.07550.07090.0897-0.00070.1589-0.01460.04840.2860.16590.3256-11.5093-51.349919.7369
200.038-0.07060.18270.0941-0.24220.59660.05860.0916-0.218-0.23270.0339-0.14220.10220.15260.00420.7228-0.15620.0670.0475-0.1850.2296-21.7279-52.4538-12.1491
210.5710.37570.53150.64030.6671.3580.0623-0.0796-0.0792-0.06390.0067-0.19420.14380.2182-0.08210.1583-0.0360.04750.19770.0710.2979-3.3745-45.932118.327
220.5638-0.43340.36211.5767-0.32390.20480.0412-0.0642-0.05940.05030.0249-0.22110.18340.34390.02680.2388-0.0660.03230.56830.15060.22194.6737-41.798432.1168
230.1182-0.1122-0.0460.2172-0.15080.49620.1442-0.0198-0.1119-0.0158-0.09360.0870.0176-0.08370.01130.2812-0.12980.04330.12950.0370.262-26.3572-47.38825.5855
240.68420.081-0.07460.4723-0.13940.23160.1135-0.1734-0.1078-0.6824-0.2005-0.09290.40130.0408-0.0109-0.286-0.16790.04820.18560.12570.2039-17.6911-40.061818.1625
250.80760.4778-1.23150.2777-0.70731.88970.0786-0.02940.0179-0.01460.00350.0422-0.02670.0416-0.05170.8837-0.17370.01680.326-0.10520.3567-22.0198-55.003-21.5916
261.12170.8762-0.22070.6817-0.17510.04750.0670.12330.0365-0.16530.12170.13510.0199-0.1789-0.02990.9539-0.06250.06860.4869-0.18430.4456-16.0997-54.845-37.178
270.91350.1106-0.29070.6594-0.02720.0922-0.06450.1689-0.1575-0.268-0.1266-0.0080.0932-0.03540.00150.48970.07130.06360.2081-0.07540.3944-12.7218-60.7133-12.3472
280.46710.24170.15420.4125-0.10070.22550.03780.0176-0.0465-0.15020.0183-0.1034-0.02340.1475-0.08150.4044-0.05140.15330.19310.02740.22543.1579-34.7927-16.9833
290.28940.02760.08920.3363-0.14810.23560.04170.03670.01530.00610.03140.04420.19480.0103-0.00220.6133-0.01260.2180.2737-0.03310.0937-5.7129-34.5724-25.909
300.54780.16760.5010.59230.66841.85630.0139-0.1166-0.0867-0.2087-0.0187-0.22380.18040.32640.01320.1219-0.03750.23020.23670.07150.35397.0059-32.49493.7941
310.21370.1250.03110.43460.17751.0309-0.1106-0.24-0.1329-0.131-0.0259-0.22280.34790.24670.05470.28190.01720.14540.25480.03490.34893.5845-35.174814.3553
320.2971-0.2279-0.05820.1149-0.11720.714-0.0049-0.3129-0.1271-0.2256-0.0049-0.2406-0.05710.13810.02030.2004-0.00120.15550.11670.05040.28490.9417-30.04068.16
330.63350.04970.3070.50960.13470.7575-0.0332-0.1410.134-0.1735-0.0396-0.1257-0.06870.1112-0.01290.2301-0.01440.12260.23530.02760.202-1.034-24.654710.2927
341.90860.951-0.79750.5759-0.17651.63940.053-0.2963-0.09930.31920.0176-0.0131-0.03580.10460.02130.2753-0.0597-0.08150.69080.01640.42856.0622-29.471255.5675
35-0.00040.00510.0017-0.0050.00020.00020.006-0.2365-0.03850.2384-0.0323-0.02630.02170.10830.02770.3945-0.077-0.09160.77290.02840.486414.9367-27.955860.5834
360.03350.07570.25110.16410.62131.9649-0.24460.1020.0108-0.1348-0.0688-0.207-0.17330.09960.05610.0413-0.1783-0.03990.73210.15690.579516.4658-31.783134.9114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 130 )A1 - 130
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 173 )A131 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 191 )A174 - 191
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 271 )A192 - 271
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 333 )A272 - 333
6X-RAY DIFFRACTION6chain 'A' and (resid 334 through 387 )A334 - 387
7X-RAY DIFFRACTION7chain 'A' and (resid 388 through 410 )A388 - 410
8X-RAY DIFFRACTION8chain 'A' and (resid 411 through 438 )A411 - 438
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 36 )B1 - 36
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 54 )B37 - 54
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 93 )B55 - 93
12X-RAY DIFFRACTION12chain 'B' and (resid 94 through 271 )B94 - 271
13X-RAY DIFFRACTION13chain 'B' and (resid 272 through 332 )B272 - 332
14X-RAY DIFFRACTION14chain 'B' and (resid 333 through 362 )B333 - 362
15X-RAY DIFFRACTION15chain 'B' and (resid 363 through 398 )B363 - 398
16X-RAY DIFFRACTION16chain 'B' and (resid 399 through 433 )B399 - 433
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 54 )C1 - 54
18X-RAY DIFFRACTION18chain 'C' and (resid 55 through 93 )C55 - 93
19X-RAY DIFFRACTION19chain 'C' and (resid 94 through 130 )C94 - 130
20X-RAY DIFFRACTION20chain 'C' and (resid 131 through 150 )C131 - 150
21X-RAY DIFFRACTION21chain 'C' and (resid 151 through 191 )C151 - 191
22X-RAY DIFFRACTION22chain 'C' and (resid 192 through 216 )C192 - 216
23X-RAY DIFFRACTION23chain 'C' and (resid 217 through 271 )C217 - 271
24X-RAY DIFFRACTION24chain 'C' and (resid 272 through 336 )C272 - 336
25X-RAY DIFFRACTION25chain 'C' and (resid 337 through 363 )C337 - 363
26X-RAY DIFFRACTION26chain 'C' and (resid 364 through 410 )C364 - 410
27X-RAY DIFFRACTION27chain 'C' and (resid 411 through 431 )C411 - 431
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 54 )D1 - 54
29X-RAY DIFFRACTION29chain 'D' and (resid 55 through 93 )D55 - 93
30X-RAY DIFFRACTION30chain 'D' and (resid 94 through 131 )D94 - 131
31X-RAY DIFFRACTION31chain 'D' and (resid 132 through 191 )D132 - 191
32X-RAY DIFFRACTION32chain 'D' and (resid 192 through 271 )D192 - 271
33X-RAY DIFFRACTION33chain 'D' and (resid 272 through 349 )D272 - 349
34X-RAY DIFFRACTION34chain 'D' and (resid 350 through 387 )D350 - 387
35X-RAY DIFFRACTION35chain 'D' and (resid 388 through 410 )D388 - 410
36X-RAY DIFFRACTION36chain 'D' and (resid 411 through 431 )D411 - 431

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