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- PDB-2w00: Crystal structure of the HsdR subunit of the EcoR124I restriction... -

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Basic information

Entry
Database: PDB / ID: 2w00
TitleCrystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP
ComponentsHSDR
KeywordsHYDROLASE / ATP-BINDING / DNA-BINDING / RESTRICTION SYSTEM / HELICASE / R.ECOR124I / NUCLEOTIDE-BINDING / TYPE I RESTRICTION-MODIFICATION ENZYME
Function / homology
Function and homology information


type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / ATP binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2110 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2040 / tt1808, chain A - #50 / Actin; Chain A, domain 4 - #50 / tt1808, chain A / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal ...Arc Repressor Mutant, subunit A - #2110 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2040 / tt1808, chain A - #50 / Actin; Chain A, domain 4 - #50 / tt1808, chain A / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal / SWI2/SNF2 ATPase / Restriction endonuclease, type I, HsdR / Actin; Chain A, domain 4 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLapkouski, M. / Panjikar, S. / Kuta Smatanova, I. / Ettrich, R. / Csefalvay, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structure of the Motor Subunit of Type I Restriction-Modification Complex Ecor124I.
Authors: Lapkouski, M. / Panjikar, S. / Janscak, P. / Smatanova, I.K. / Carey, J. / Ettrich, R. / Csefalvay, E.
History
DepositionAug 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HSDR
B: HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,0286
Polymers241,9652
Non-polymers1,0634
Water10,485582
1
A: HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5143
Polymers120,9821
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5143
Polymers120,9821
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.910, 129.922, 161.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A13 - 141
2111B13 - 141
1211A148 - 181
2211B148 - 181
1311A190 - 584
2311B191 - 584
1411A591 - 858
2411B591 - 858
1511A870 - 885
2511B870 - 885

NCS oper: (Code: given
Matrix: (-1, -0.0031, -0.0037), (0.0031, -0.9998, -0.0183), (-0.0037, -0.0184, 0.9998)
Vector: 62.3129, 31.8595, 0.3459)

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Components

#1: Protein HSDR / R.ECOR124I


Mass: 120982.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: B834(DE3) / Plasmid: PTRC124 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q304R3, UniProt: P10486*PLUS, type I site-specific deoxyribonuclease
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE TAKEN FROM THE NCBI PROTEIN DATABASE

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1 UL OF PROTEIN IN 20 MM PHOSPHATE PH 7.5, 100 MM KCL, 5 MM ATP WAS MIXED WITH 2 UL OF RESERVOIR, CONTAINING 0.2 M LI2SO4, 8 % PEG 20K, 8 % PEG 550 MME, 1.5 MM DTT, 277 K, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9784
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI HORYSONTAL FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 80316 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→19.97 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.401 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 977 1.2 %RANDOM
Rwork0.221 ---
obs0.221 79250 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13740 0 64 582 14386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02214076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.95118997
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.28651684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13324.619734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.712152517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0971586
X-RAY DIFFRACTIONr_chiral_restr0.2140.22077
X-RAY DIFFRACTIONr_gen_planes_refined00.0210682
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.26913
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3350.29696
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3290.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3911.58541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.036213581
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.62536128
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2864.55416
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6771 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.110.05
tight thermal0.440.5
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.399 68
Rwork0.28 5681
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)
16.1633-4.3576-5.48147.62335.604510.2060.3004-0.03761.2221-0.6451-0.07530.0599-1.21650.1969-0.2251-0.08-0.0527-0.0535-0.17690.00550.238143.616160.686728.7924
25.05491.3325-0.5091.8139-0.40990.71750.0718-0.15450.47520.0212-0.14450.0234-0.01140.03460.0728-0.1338-0.0084-0.025-0.11840.028-0.067421.667647.083226.5107
37.47530.9382.41981.8598-0.91062.2022-0.1145-0.318-0.6-0.16750.11740.02730.237-0.0522-0.0029-0.1366-0.03230.0002-0.1635-0.003-0.080624.666131.041228.9129
45.12352.99911.00634.90211.34181.81540.02320.08780.3937-0.1235-0.05170.05920.0397-0.08160.0285-0.180.0295-0.0181-0.14640.028-0.059927.296143.255525.9649
511.2233-3.6062-4.264510.7804-0.76892.0959-0.1763-1.08380.53280.92850.5054-0.7346-0.23160.2586-0.32910.0546-0.0524-0.02020.0393-0.16580.091244.770453.653843.8072
665.847112.90044.53814.62724.5757.7287-0.1411-3.97810.8062-0.8528-0.882-0.0033-0.0875-0.5261.02310.3970.1363-0.01560.20590.03560.222636.483643.745945.2276
72.2577-0.00550.02651.13550.6340.3543-0.0076-0.09670.2010.13110.0049-0.10980.1140.05990.0027-0.1176-0.0026-0.0095-0.11240.0022-0.132944.741744.165329.8257
83.37730.77280.38234.22740.76765.69480.02010.50590.1665-0.70150.05370.0529-0.06050.1316-0.0737-0.08130.03680.0182-0.10510.009-0.273754.016335.834311.9863
91.5887-0.0179-0.14433.9667-0.30742.215-0.00130.3655-0.3726-0.3886-0.01880.07160.2741-0.0190.02010.0075-0.00560.00630.0152-0.0526-0.105852.571319.608814.0972
101.39780.90130.50195.68763.34873.7116-0.0470.4017-0.1559-0.62380.3546-0.7870.03180.7226-0.3076-0.02760.0140.10210.1028-0.0021-0.094565.096531.486412.7141
112.73190.01960.57393.0302-0.141.23590.2248-0.1756-0.53920.1993-0.1055-0.5190.36510.1318-0.11920.0111-0.0124-0.1113-0.07820.03420.076871.534918.830142.8017
121.2359-0.9096-4.467510.23591.997916.3224-0.15030.0613-0.5374-0.06850.0038-0.77841.714-0.36190.14650.1467-0.0462-0.0571-0.1421-0.01120.062656.98518.364832.6704
134.15960.2796-0.12153.26610.02321.86680.14080.1554-0.2225-0.0561-0.0865-0.2520.2049-0.0124-0.0544-0.1443-0.0183-0.0511-0.1911-0.0174-0.198864.488926.925937.9801
142.1529-0.683-0.21585.41743.71823.63120.09540.00950.0734-0.0783-0.0856-0.1705-0.3476-0.1382-0.0097-0.2055-0.0554-0.0376-0.08020.0397-0.032573.781743.644940.9288
1520.464-3.8196-11.82618.608915.322836.4015-0.3534-1.80390.83041.3642-0.39280.5854-0.8191-1.83090.74610.45060.0375-0.03370.4489-0.1332-0.201760.042854.286966.897
1627.0502-11.0783-5.06659.03743.72135.7301-0.2309-0.29741.38921.0699-0.1396-0.471-1.093-0.52740.37050.38470.0779-0.08050.1365-0.0728-0.198155.981652.850259.0073
173.2771-2.77680.10416.8253-3.266411.2876-0.1539-0.9323-0.39591.6658-0.166-0.21310.11220.95780.31980.3682-0.149-0.24460.23650.13450.079676.161134.279362.4186
187.1551-6.42560.21098.9297-0.09995.5535-0.681-0.5109-0.87261.4392-0.06351.2719-0.3189-0.76180.74460.3159-0.03980.160.3775-0.12240.130351.579647.248159.8765
198.924-4.7286.70914.6066-3.42759.77150.5301-0.3997-2.5213-0.22640.45780.61921.1953-0.4358-0.988-0.0038-0.1295-0.0517-0.087-0.00630.624618.4061-29.250227.8012
205.82761.85281.26932.36030.99420.47340.0837-0.0806-0.58450.0615-0.1429-0.08550.0868-0.05590.0593-0.09170.0087-0.0021-0.0894-0.0667-0.11740.3845-15.611125.85
2134.56852.2665-18.61331.15862.407123.0510.0602-1.25081.06360.14720.22890.0183-0.8351.0685-0.2891-0.0984-0.0109-0.1027-0.1202-0.0667-0.201846.062-0.155130.258
224.79121.22840.11883.21250.21330.8424-0.05620.1731-0.1553-0.14150-0.122-0.0292-0.01130.0562-0.1530.0184-0.0271-0.1214-0.0009-0.18634.8863-7.171126.4711
2310.0489-7.3387-2.42069.8439-0.50571.7357-0.5168-1.1755-1.62830.39260.15230.29360.1766-0.28070.36450.050.01610.00960.20340.19750.147917.1859-22.55142.9637
24211.699768.3902-90.31122.408-30.26642.31162.2523-4.936-1.1761-0.5075-2.28050.0709-0.1791.78230.02820.37130.18280.11590.357-0.01020.423624.5536-13.339644.8261
253.38320.0341-0.18531.1001-0.230.0575-0.0705-0.1548-0.26170.14240.04770.1083-0.0758-0.01640.0228-0.0913-0.008-0.0147-0.0876-0.0071-0.185417.5139-12.812229.6167
263.23511.8086-1.01984.5638-0.12325.8174-0.03630.6349-0.1141-0.69720.1620.0147-0.0937-0.3209-0.1257-0.0740.0073-0.0833-0.0234-0.0254-0.31877.9933-4.358511.7047
271.5582-0.3653-0.64525.0170.18452.5893-0.04940.38150.4685-0.37570.11250.1779-0.22570.0254-0.0631-0.0206-0.0695-0.08940.03960.0429-0.09878.369411.570213.997
282.22130.728-0.28626.3983-4.14144.4592-0.07970.5997-0.0801-0.66360.32490.80290.0996-0.618-0.2451-0.0118-0.0522-0.15660.0885-0.0153-0.1272-2.7256-1.137611.6285
292.56990.0897-0.72452.86370.07751.60160.2255-0.16870.57490.2235-0.01040.7006-0.4438-0.1356-0.2151-0.00650.0040.1161-0.071-0.01180.1787-9.386312.38942.6428
300.447-0.30013.036912.5107-0.042320.9572-0.06410.19630.4231-0.08670.03730.6384-1.6961-0.16150.02680.0585-0.03420.0725-0.13640.02960.15195.15523.037532.6775
314.13930.70790.25423.4097-0.65282.04850.13060.0970.2945-0.0350.00870.3897-0.2302-0.0136-0.1393-0.1559-0.01380.0371-0.2020.0218-0.1213-3.5034.444837.7889
323.0341-0.35931.39455.771-6.57139.7831-0.0220.0302-0.159-0.2835-0.03060.12230.66080.19040.0527-0.1519-0.0360.0376-0.1316-0.0414-0.0425-11.1798-13.968940.1858
3312.1902-2.68883.51592.2796-3.5275.58890.0412-0.4433-1.02640.0746-0.08480.08710.38980.50950.04360.28180.00660.05160.05940.0416-0.14094.2578-22.663261.9162
344.5089-2.1245-0.44784.33871.625811.6647-0.0604-1.16060.5481.3698-0.00260.6838-0.1807-0.97440.06310.2924-0.10250.24950.2478-0.12080.2246-14.0124-3.315361.5702
3519.7316-6.5319-2.50399.18741.45737.8573-0.2981-0.93861.01910.44730.1185-0.770.39560.75290.17960.2077-0.0155-0.11760.1010.1112-0.047410.4293-15.055262.7732
361.61690.01391.47580.60742.10788.5753-0.1338-0.4466-0.0085-0.247-0.216-0.3652-0.07250.85640.34980.0651-0.0544-0.00450.24050.1357-0.079212.7442-13.048855.0299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 40
2X-RAY DIFFRACTION2A41 - 81
3X-RAY DIFFRACTION3A82 - 113
4X-RAY DIFFRACTION4A114 - 164
5X-RAY DIFFRACTION5A165 - 177
6X-RAY DIFFRACTION6A178 - 192
7X-RAY DIFFRACTION7A193 - 283
8X-RAY DIFFRACTION8A284 - 327
9X-RAY DIFFRACTION9A328 - 407
10X-RAY DIFFRACTION10A408 - 464
11X-RAY DIFFRACTION11A465 - 625
12X-RAY DIFFRACTION12A626 - 640
13X-RAY DIFFRACTION13A641 - 703
14X-RAY DIFFRACTION14A704 - 754
15X-RAY DIFFRACTION15A755 - 770
16X-RAY DIFFRACTION16A771 - 788
17X-RAY DIFFRACTION17A789 - 837
18X-RAY DIFFRACTION18A838 - 885
19X-RAY DIFFRACTION19B13 - 40
20X-RAY DIFFRACTION20B41 - 81
21X-RAY DIFFRACTION21B82 - 87
22X-RAY DIFFRACTION22B88 - 164
23X-RAY DIFFRACTION23B165 - 177
24X-RAY DIFFRACTION24B178 - 192
25X-RAY DIFFRACTION25B193 - 281
26X-RAY DIFFRACTION26B282 - 326
27X-RAY DIFFRACTION27B327 - 418
28X-RAY DIFFRACTION28B419 - 464
29X-RAY DIFFRACTION29B465 - 625
30X-RAY DIFFRACTION30B626 - 640
31X-RAY DIFFRACTION31B641 - 707
32X-RAY DIFFRACTION32B708 - 754
33X-RAY DIFFRACTION33B755 - 787
34X-RAY DIFFRACTION34B788 - 836
35X-RAY DIFFRACTION35B837 - 860
36X-RAY DIFFRACTION36B861 - 892

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