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Basic information

Entry
Database: PDB / ID: 4elb
TitleStructure-activity relationship guides enantiomeric preference among potent inhibitors of B. anthracis dihydrofolate reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / dihydrofolate reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-34R / Chem-34S / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBourne, C.R. / Barrow, W.W.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase.
Authors: Bourne, C.R. / Wakeham, N. / Nammalwar, B. / Tseitin, V. / Bourne, P.C. / Barrow, E.W. / Mylvaganam, S. / Ramnarayan, K. / Bunce, R.A. / Berlin, K.D. / Barrow, W.W.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,73434
Polymers156,9248
Non-polymers5,81026
Water11,169620
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A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2124
Polymers19,6151
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
H: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2124
Polymers19,6151
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2124
Polymers19,6151
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2124
Polymers19,6151
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2124
Polymers19,6151
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7325
Polymers19,6151
Non-polymers1,1174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2124
Polymers19,6151
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7325
Polymers19,6151
Non-polymers1,1174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.874, 135.444, 168.194
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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Protein , 1 types, 8 molecules AHCBGFDE

#1: Protein
Dihydrofolate reductase


Mass: 19615.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: A thrombin cut site was engineered between the C-terminus and the 6 x His tag
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: sterne / Gene: BAS2083, BA_2237, dfrA, DHFR, GBAA_2237 / Plasmid: pCR-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81R22, dihydrofolate reductase

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Non-polymers , 5 types, 646 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-34S / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-phenylphthalazin-2(1H)-yl]prop-2-en-1-one / (S,E)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-phenylphthalazin-2(1H)-yl)prop-2-en-1-one


Mass: 520.582 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H28N6O3
#5: Chemical
ChemComp-34R / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1R)-1-phenylphthalazin-2(1H)-yl]prop-2-en-1-one / (R,E)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-phenylphthalazin-2(1H)-yl)prop-2-en-1-one


Mass: 520.582 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H28N6O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 16-22% PEG 3350, 0.2M CaCl2, 0.1M MES, +/- 3% glycerol, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 48511 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.192 / Net I/σ(I): 14.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FL8
Resolution: 2.6→47.94 Å / SU ML: 1.13 / σ(F): 1.49 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3094 2459 5.08 %
Rwork0.2435 --
obs0.2469 48426 99.82 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.858 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5331 Å20 Å2-0 Å2
2--0.2709 Å20 Å2
3----4.804 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11028 0 406 620 12054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711795
X-RAY DIFFRACTIONf_angle_d1.07815987
X-RAY DIFFRACTIONf_dihedral_angle_d19.9044460
X-RAY DIFFRACTIONf_chiral_restr0.0661602
X-RAY DIFFRACTIONf_plane_restr0.0062032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.37941360.32872491X-RAY DIFFRACTION100
2.65-2.70410.40581520.31522522X-RAY DIFFRACTION100
2.7041-2.76290.42641410.28882488X-RAY DIFFRACTION100
2.7629-2.82720.3611330.29352554X-RAY DIFFRACTION100
2.8272-2.89790.39041300.26162502X-RAY DIFFRACTION100
2.8979-2.97620.34011300.27332548X-RAY DIFFRACTION100
2.9762-3.06380.35341240.25222527X-RAY DIFFRACTION100
3.0638-3.16260.35511180.25632533X-RAY DIFFRACTION100
3.1626-3.27560.34631450.2382547X-RAY DIFFRACTION100
3.2756-3.40680.28821470.2432531X-RAY DIFFRACTION100
3.4068-3.56180.32851240.25792560X-RAY DIFFRACTION100
3.5618-3.74950.33081250.24372566X-RAY DIFFRACTION100
3.7495-3.98430.30671290.21792585X-RAY DIFFRACTION100
3.9843-4.29170.27131460.20142536X-RAY DIFFRACTION100
4.2917-4.72330.23891420.18022571X-RAY DIFFRACTION100
4.7233-5.40590.23831550.20762589X-RAY DIFFRACTION100
5.4059-6.80780.29261420.26382628X-RAY DIFFRACTION100
6.8078-47.94850.28221400.27692689X-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)
11.16540.49680.22220.71380.30512.3840.1460.02150.01740.04050.0839-0.0519-0.14540.2863-0.05240.0384-0.0331-0.00660.06970.02630.079115.9348-33.3281-3.4827
21.12790.5098-0.72743.02130.55961.70050.0935-0.07380.1441-0.00310.0135-0.3492-0.09230.23980.00070.0645-0.11320.04220.13520.02540.159721.1777-23.9957-15.0548
31.3679-0.1990.06351.499-0.4742.0989-0.03610.02680.1333-0.11720.14910.177-0.1139-0.1777-0.07480.025-0.0113-0.04530.07230.05740.143810.0109-33.884-9.0433
40.4505-0.0797-0.23850.8480.07760.98180.05450.17960.1144-0.15890.04640.2065-0.2609-0.28250.05890.13310.0895-0.04730.1526-0.00530.098210.7212-42.3411-5.6322
50.9380.23370.38211.1761-0.24762.07130.04210.0722-0.139-0.25840.1202-0.01450.3407-0.0803-0.13580.2280.0586-0.05110.0768-0.01020.10987.257-2.52742.1886
60.00990.00170.0240.769-0.94711.2379-0.11170.1484-0.2381-0.1392-0.1285-0.1940.10630.19580.02660.16320.07980.07880.1719-0.02620.18218.7136-5.94976.5181
70.33610.0302-0.16090.6807-0.65321.1558-0.02370.0054-0.0485-0.0481-0.0337-0.07130.0566-0.01560.02830.10160.13690.01430.1339-0.04550.054410.3314-0.7149.1926
82.1373-3.586-0.34317.98083.94755.8442-0.17710.7988-0.7455-0.53730.0929-0.45540.57930.30030.03090.3557-0.07340.08520.3629-0.22030.46532.82719.139722.1812
90.22970.1557-0.24110.7222-0.17411.35830.004-0.0304-0.06330.10770.0655-0.01090.1096-0.0596-0.0210.15740.1505-0.0220.1425-0.01860.126419.2416-38.281739.2366
101.56650.1246-0.7521.54730.27391.7484-0.0969-0.11890.12540.20.0570.291-0.1363-0.35230.07390.12630.14020.03090.1236-0.01720.17529.1776-32.021127.1683
110.4371-0.08270.33580.3757-0.13911.18070.04370.0194-0.04940.08410.0423-0.0280.05570.0999-0.01970.08070.1046-0.02460.04010.01070.087724.0807-40.92934.9757
127.39494.082-2.36242.5819-2.12832.8214-0.0379-0.285-0.16080.82160.08720.85390.207-0.2487-0.01090.3834-0.10310.05850.28230.14180.347342.3656-48.940517.827
130.70060.49710.04810.6726-0.49941.32680.0207-0.08650.16730.1761-0.0027-0.0168-0.26740.2511-0.04270.0871-0.006-0.05710.0811-0.05680.160411.885234.1321-4.6989
141.1999-0.08-0.49171.64620.25241.62540.0523-0.22030.33550.1199-0.0551-0.4243-0.43420.3825-0.05670.1878-0.0821-0.04620.12820.00680.198816.320842.5644-15.6431
150.5471-0.3090.32520.4995-0.71781.5725-0.0349-0.1062-0.0391-0.05880.00330.0357-0.097-0.4329-0.00980.04870.0586-0.05580.1155-0.03830.09816.688528.0646-4.9582
161.90432.18741.48946.52425.92286.29330.06320.5891-0.9007-0.34-0.08150.05060.63130.02410.01190.54210.04520.12950.2181-0.08970.49673.695414.5256-22.633
170.4333-0.34820.432.1568-0.06451.3267-0.0275-0.19130.09060.0664-0.00680.2643-0.2996-0.3183-0.09010.1150.02750.01350.1881-0.03870.113514.192729.638638.5605
183.08330.6987-0.71071.5844-0.81291.4910.0302-0.27180.43610.2153-0.06250.3852-0.2662-0.48110.05050.24530.10390.02940.288-0.03380.19841.776132.896328.2562
190.79750.02580.57010.5450.01891.44350.0022-0.0212-0.03740.085-0.0138-0.0561-0.0341-0.04340.00750.04720.0143-0.04810.0001-0.01310.079318.488926.751234.3132
203.92591.7593-3.90240.7884-1.74873.8789-0.0551-0.1920.09870.4897-0.32540.86-0.0131-0.68090.3930.5734-0.00360.04030.3537-0.08690.40236.336920.625119.3826
210.4918-0.2820.27361.10650.42341.68450.0013-0.0873-0.0480.0774-0.00190.0704-0.1425-0.2797-0.00350.05490.0386-0.00780.138-0.05630.0746-17.1761-5.802741.03
221.12430.8488-0.87531.4184-0.2132.0749-0.0242-0.14150.40480.0696-0.06650.4186-0.3714-0.5520.05640.26940.1835-0.07450.3608-0.12180.2122-26.73410.190428.4073
230.22950.20680.46630.46630.20151.246-0.04850.0889-0.1486-0.01880.0068-0.08620.1076-0.06650.01780.04690.010.08250.1153-0.14620.1046-11.9323-8.841437.8117
244.7772-1.8995-4.2012.56620.64964.2694-0.10920.0345-0.12470.3423-0.55530.86470.0247-0.56110.66310.36270.0289-0.01750.4357-0.2160.5463.116-13.899518.6837
250.41680.20210.32110.25270.13190.4648-0.1482-0.06480.29380.014-0.07710.1132-0.3709-0.09130.00130.2044-0.0859-0.18140.0704-0.09390.1128-19.83863.5762-3.9129
260.6467-0.0530.17461.2638-0.08481.1579-0.22080.06880.3780.0515-0.1096-0.1551-0.47920.0872-0.04230.2944-0.0691-0.19880.12330.0230.2273-20.82417.7555-16.6924
271.1688-0.33050.75721.0564-0.09822.8551-0.131-0.0708-0.0009-0.10650.0640.3173-0.2554-0.36910.10750.1896-0.0889-0.00990.0812-0.01520.1517-25.7032-7.0923-1.7013
280.7630.23120.49280.94790.30960.8098-0.03350.2792-0.2206-0.1822-0.07870.07460.1655-0.1737-0.0370.2482-0.0935-0.02850.2152-0.07930.0887-24.3646-13.4261-7.4838
290.81120.0482-0.01351.0847-0.17861.98590.013-0.0065-0.05050.15290.0715-0.1073-0.17350.2793-0.08730.1401-0.029-0.04060.09630.01930.05117.7072-3.320145.294
300.5804-0.199-0.44520.43820.41371.35260.02360.32170.2291-0.22460.1069-0.6539-0.19010.5647-0.07450.3943-0.14120.01540.8115-0.09680.645230.94870.924352.6006
310.7382-0.37680.35540.6903-0.18931.6224-0.1119-0.1397-0.01840.12650.0745-0.07730.17340.16260.04780.05930.04020.03520.09180.08250.045313.9855-6.045649.7657
323.32451.7276-4.79340.8975-2.49056.9107-0.203-0.2143-0.4054-0.1294-0.0715-0.20860.5856-0.2730.27770.71670.06330.30720.34260.10120.4598-0.9754-11.825365.962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:39)
2X-RAY DIFFRACTION2(chain A and resid 40:96)
3X-RAY DIFFRACTION3(chain A and resid 97:122)
4X-RAY DIFFRACTION4(chain A and resid 123:166)
5X-RAY DIFFRACTION5(chain B and resid 1:25)
6X-RAY DIFFRACTION6(chain B and resid 26:62)
7X-RAY DIFFRACTION7(chain B and resid 63:160)
8X-RAY DIFFRACTION8(chain B and resid 161:166)
9X-RAY DIFFRACTION9(chain C and resid 1:36)
10X-RAY DIFFRACTION10(chain C and resid 37:87)
11X-RAY DIFFRACTION11(chain C and resid 88:161)
12X-RAY DIFFRACTION12(chain C and resid 162:166)
13X-RAY DIFFRACTION13(chain D and resid 1:45)
14X-RAY DIFFRACTION14(chain D and resid 46:99)
15X-RAY DIFFRACTION15(chain D and resid 100:158)
16X-RAY DIFFRACTION16(chain D and resid 159:166)
17X-RAY DIFFRACTION17(chain E and resid 1:40)
18X-RAY DIFFRACTION18(chain E and resid 41:82)
19X-RAY DIFFRACTION19(chain E and resid 83:160)
20X-RAY DIFFRACTION20(chain E and resid 161:166)
21X-RAY DIFFRACTION21(chain F and resid 1:35)
22X-RAY DIFFRACTION22(chain F and resid 36:94)
23X-RAY DIFFRACTION23(chain F and resid 95:160)
24X-RAY DIFFRACTION24(chain F and resid 161:166)
25X-RAY DIFFRACTION25(chain G and resid 1:62)
26X-RAY DIFFRACTION26(chain G and resid 63:109)
27X-RAY DIFFRACTION27(chain G and resid 110:149)
28X-RAY DIFFRACTION28(chain G and resid 150:166)
29X-RAY DIFFRACTION29(chain H and resid 1:43)
30X-RAY DIFFRACTION30(chain H and resid 44:80)
31X-RAY DIFFRACTION31(chain H and resid 81:159)
32X-RAY DIFFRACTION32(chain H and resid 160:166)

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