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- PDB-5f2l: Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in... -

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Basic information

Entry
Database: PDB / ID: 5f2l
TitleTagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with competitive inhibitor talitol-1,6-bisphosphate
ComponentsTagatose 1,6-diphosphate aldolase 2
KeywordsLYASE / Covalent intermediate / Substrate / Aldolase / Class I
Function / homology
Function and homology information


tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity
Similarity search - Function
Tagatose 1,6-diphosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D-MANNITOL-1,6-DIPHOSPHATE / Tagatose 1,6-diphosphate aldolase 2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.755 Å
AuthorsLowKam, C.
CitationJournal: To Be Published
Title: NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE
Authors: LowKam, C. / Liotard, B. / Sygusch, J.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 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_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tagatose 1,6-diphosphate aldolase 2
C: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,27016
Polymers146,4824
Non-polymers78812
Water25,2751403
1
A: Tagatose 1,6-diphosphate aldolase 2
D: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7587
Polymers73,2412
Non-polymers5175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tagatose 1,6-diphosphate aldolase 2
B: Tagatose 1,6-diphosphate aldolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5129
Polymers73,2412
Non-polymers2717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.966, 108.029, 237.423
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, 4 molecules ACBD

#1: Protein
Tagatose 1,6-diphosphate aldolase 2 / D-tagatose-1 / 6-bisphosphate aldolase 2 / Tagatose-bisphosphate aldolase 2


Mass: 36620.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: lacD2, lacD.2, SPy_1919, M5005_Spy1635 / Production host: Escherichia coli (E. coli) / References: UniProt: P63705, tagatose-bisphosphate aldolase

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Non-polymers , 5 types, 1415 molecules

#2: Chemical ChemComp-M2P / D-MANNITOL-1,6-DIPHOSPHATE / 1,6-DI-O-PHOSPHONO-D-MANNITOL


Mass: 342.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O12P2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1403 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris Acetate, Calcium Acetate, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.755→45.187 Å / Num. obs: 155209 / % possible obs: 94.14 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 8.8
Reflection shellResolution: 1.755→1.799 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.31 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHF
Resolution: 1.755→45.187 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 1897 1.28 %
Rwork0.1625 --
obs0.1629 148122 89.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.755→45.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10228 0 34 1403 11665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810616
X-RAY DIFFRACTIONf_angle_d1.07214359
X-RAY DIFFRACTIONf_dihedral_angle_d13.2353978
X-RAY DIFFRACTIONf_chiral_restr0.0421594
X-RAY DIFFRACTIONf_plane_restr0.0051864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7554-1.79930.322650.30915535X-RAY DIFFRACTION48
1.7993-1.8480.30471010.2787587X-RAY DIFFRACTION66
1.848-1.90230.27741080.25198751X-RAY DIFFRACTION76
1.9023-1.96370.22711300.2299645X-RAY DIFFRACTION84
1.9637-2.03390.25431340.207710601X-RAY DIFFRACTION92
2.0339-2.11540.20621450.18611176X-RAY DIFFRACTION97
2.1154-2.21160.2121460.178811337X-RAY DIFFRACTION98
2.2116-2.32820.20481510.172811377X-RAY DIFFRACTION99
2.3282-2.47410.22281490.161811488X-RAY DIFFRACTION99
2.4741-2.66510.17761530.160411578X-RAY DIFFRACTION100
2.6651-2.93320.18061500.162511609X-RAY DIFFRACTION100
2.9332-3.35760.17741540.152611695X-RAY DIFFRACTION100
3.3576-4.22970.16021530.130211761X-RAY DIFFRACTION100
4.2297-45.2020.17121580.149112085X-RAY DIFFRACTION99
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)
13.50010.55971.32145.8258-1.47795.03150.14350.0264-0.0911-0.1852-0.1639-0.06090.0727-0.0642-0.01560.11770.0420.03050.2592-0.03040.219262.717756.596535.2657
23.4342-1.194-0.15257.70220.68760.9003-0.39840.1230.9805-0.9971-0.07330.8876-1.742-0.58730.2441.2770.2762-0.32930.65160.00690.942261.293185.79128.6033
31.8071-0.12320.24631.1147-0.84232.3856-0.13450.320.5921-0.0405-0.0631-0.2681-0.34330.30630.19540.3125-0.02540.00380.26330.06960.390966.478869.236328.5187
41.8429-0.0367-0.38810.73420.53831.42980.04130.19130.1586-0.09560.01430.0783-0.1316-0.0702-0.04670.20580.03550.0010.21410.05540.237748.35462.644127.617
51.6068-1.93392.31215.6993-2.50097.3654-0.0738-0.05590.71590.0026-0.320.0398-0.7439-0.49510.10040.23150.0841-0.02330.1348-0.00570.52441.395578.453342.6918
62.2534-0.6933-0.43660.93091.4763.10860.0560.07760.2962-0.0624-0.04350.0402-0.0844-0.1198-0.02610.16680.02270.01140.13590.02520.235145.165261.619440.6104
74.615-1.8869-1.4255.41040.6637.2605-0.0509-0.52740.49630.5466-0.17760.095-0.3991-0.2350.06270.24570.0433-0.01780.2944-0.15110.380647.31574.254956.2928
82.79871.30910.48712.26450.40442.1836-0.0396-0.14270.3769-0.0339-0.03750.0679-0.2553-0.0350.01470.21730.0269-0.0030.1684-0.00930.286855.885565.470547.0331
90.1284-0.71570.42384.2507-2.49021.4706-0.6110.22790.7965-0.0618-0.0458-0.4031-1.73190.39130.1850.9552-0.1661-0.20640.4070.06730.725374.084180.753937.1893
106.139-1.92840.73793.20142.18392.92-0.1367-0.2020.3673-0.11230.0237-0.0519-0.0963-0.02210.06150.14460.0153-0.00590.1847-0.00660.129365.189761.578748.6033
113.3789-0.7305-1.20015.1759-2.23434.53960.16540.08920.13320.0455-0.14770.0388-0.11350.0543-0.01890.0964-0.0235-0.0220.2124-0.01510.206930.864453.156648.2185
120.19220.04090.02190.0198-0.00230.0021-0.5415-0.1488-1.3013-0.0996-0.00060.17121.08490.0517-0.06050.69810.05070.34590.32230.12080.873933.506726.267457.952
132.51230.1494-0.09620.5976-0.59111.33470.0169-0.2578-0.31930.0011-0.0687-0.04720.0810.15550.08650.210.02070.01140.1390.03240.25829.62441.226555.3456
143.65050.71280.61831.62090.72.01270.0319-0.169-0.04250.0649-0.0140.04550.01550.0248-0.0210.1482-0.00720.01840.09530.04850.17516.863148.277855.208
151.33070.4392-2.01825.34432.27975.912-0.58590.1544-0.87440.0249-0.2243-0.02280.7213-0.23510.54980.3873-0.08560.09660.1985-0.06510.56438.751231.074241.6511
162.07440.798-0.03422.41381.18852.9734-0.10180.0997-0.2557-0.1240.07140.09490.1428-0.06360.00010.1577-0.0248-0.00050.11210.00460.216513.20946.991942.3876
170.7139-0.0567-0.19321.88771.04190.6293-0.27440.8548-0.6888-0.6299-0.0820.3070.6929-0.6557-0.30660.509-0.1290.08760.3391-0.22060.463415.315935.194226.6047
183.7876-1.268-0.91482.0060.15063.5212-0.14210.2617-0.3045-0.0539-0.0320.11370.42490.06840.03350.2476-0.01250.02840.1623-0.01110.247323.24444.023935.9176
192.023-0.99360.87632.1675-1.59441.206-0.73010.1105-0.7352-0.2784-0.22-0.19191.37530.4279-1.7730.68060.12780.3360.24540.04920.653942.012629.558246.8198
207.60950.8717-0.60582.00282.19836.6270.00810.5734-0.133-0.25840.08270.1659-0.10020.3164-0.04190.1396-0.00690.01580.24330.01980.131432.99548.425234.7982
216.7033-0.0381-3.46024.03170.89487.0190.0808-0.40750.2972-0.01920.1617-0.352-0.45790.1554-0.18670.4087-0.01480.05880.344-0.1220.31778.386970.100174.1451
228.4764.39160.87429.7635-0.59023.23260.2347-0.4053-1.0711-0.4149-0.28980.05941.4816-1.1070.03981.2298-0.3849-0.05240.89080.00580.7879-12.064448.61777.4095
235.7194-2.9997-1.17975.22663.24614.38010.4071-0.1745-0.3663-0.1766-0.3410.3933-0.1708-1.110.13390.30970.00760.04430.4518-0.03640.274-6.24362.246573.258
242.35241.9189-0.1583.1256-0.6315.34650.0566-0.19390.03610.1488-0.02810.2916-0.2362-0.207-0.07390.161-0.07390.0750.2438-0.01320.14083.282956.251373.0654
252.7276-1.85411.96394.0294-3.00346.054-0.0326-0.289-0.16740.2456-0.0724-0.03830.180.16930.09180.1906-0.04190.06090.23450.0180.218911.313249.981772.7181
265.9606-4.81113.19864.4072-3.97236.22050.1125-0.2464-0.00320.1035-0.04690.1061-0.01750.29530.00170.1708-0.04730.03980.2174-0.04090.193717.841654.741768.785
271.25610.0592-0.77162.4184-1.7995.434-0.0345-0.7156-0.07130.37190.1180.00020.13650.4185-0.10230.3068-0.00160.03880.490.02510.2115.777152.858185.5689
281.2449-0.6731-1.29561.143-0.21824.1655-0.029-0.71820.03790.37050.171-0.0735-0.12870.2769-0.14040.4939-0.09290.08140.7632-0.08310.273410.859461.343495.3415
295.46162.42461.79174.3946-2.26477.96570.5435-0.904-0.10950.2034-0.11970.91131.5182-2.3207-0.23250.7911-0.2810.07811.22420.01060.5118-15.347259.979683.5823
302.1842-0.48721.8473.73632.15273.48780.2281-1.48060.60360.1948-0.03090.0517-0.3957-0.042-0.31790.5554-0.0530.1630.4835-0.12120.34333.760472.021487.2914
314.3795-2.37514.16318.2778-0.39399.196-0.00590.1521-0.26130.1380.2612-0.13760.4091-0.1296-0.29030.3725-0.0678-0.00850.369-0.02370.202141.465538.51539.4859
325.614-2.631.29116.14470.60130.61250.14220.02341.24390.1782-0.23780.4353-1.4666-1.32880.04821.15180.43740.06231.40340.13150.707720.175759.56415.8956
334.13731.63450.94092.03011.38293.09850.24860.203-0.08150.3217-0.12330.21720.438-1.0661-0.090.297-0.0696-0.03150.63580.04730.211429.362947.835310.1929
342.29831.8896-1.983.0381-1.88965.3657-0.07450.35130.2107-0.21610.0752-0.0145-0.2825-0.0128-0.01770.22420.0392-0.05380.3510.05990.232343.30558.649410.7811
354.55864.8193-2.19436.8024-2.84514.2290.01150.20710.0960.07120.13560.0537-0.10910.1171-0.08940.17050.0462-0.01910.31-0.01710.179849.584353.953213.896
360.0788-0.24090.65022.6131-1.51686.5045-0.14290.53220.1821-0.51210.2950.0249-0.27770.2689-0.10690.406-0.1193-0.0480.56280.07630.252348.440158.9998-5.0549
370.0725-0.05340.48540.45380.06614.6864-0.14820.53390.0209-0.33680.2740.0482-0.22960.0687-0.0320.4488-0.117-0.080.63940.08750.262944.790151.8739-8.6006
381.64280.0972.08561.4546-0.73393.1069-0.14540.32270.0204-0.16510.355-0.08580.0308-0.1098-0.11940.4613-0.0632-0.05760.68250.0020.236741.966945.5719-8.1622
391.3535-0.20190.85780.4734-0.00790.70510.0942-0.1737-0.0163-0.06430.00890.3328-0.0467-1.5414-0.14840.5014-0.0342-0.12661.52730.01250.347422.22942.6886-2.5401
405.16284.3107-5.41243.6263-4.58596.0083-0.0248-0.3735-0.4386-0.4295-0.2947-0.26380.04282.65680.12990.5682-0.0498-0.02110.6685-0.09720.380148.900434.66073.0134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:30)
2X-RAY DIFFRACTION2(chain A and resid 31:44)
3X-RAY DIFFRACTION3(chain A and resid 45:97)
4X-RAY DIFFRACTION4(chain A and resid 98:169)
5X-RAY DIFFRACTION5(chain A and resid 170:180)
6X-RAY DIFFRACTION6(chain A and resid 181:210)
7X-RAY DIFFRACTION7(chain A and resid 211:233)
8X-RAY DIFFRACTION8(chain A and resid 234:284)
9X-RAY DIFFRACTION9(chain A and resid 285:306)
10X-RAY DIFFRACTION10(chain A and resid 307:324)
11X-RAY DIFFRACTION11(chain B and resid 3:29)
12X-RAY DIFFRACTION12(chain B and resid 30:52)
13X-RAY DIFFRACTION13(chain B and resid 53:110)
14X-RAY DIFFRACTION14(chain B and resid 111:168)
15X-RAY DIFFRACTION15(chain B and resid 169:179)
16X-RAY DIFFRACTION16(chain B and resid 180:211)
17X-RAY DIFFRACTION17(chain B and resid 212:233)
18X-RAY DIFFRACTION18(chain B and resid 234:280)
19X-RAY DIFFRACTION19(chain B and resid 281:307)
20X-RAY DIFFRACTION20(chain B and resid 308:324)
21X-RAY DIFFRACTION21(chain C and resid 2:27)
22X-RAY DIFFRACTION22(chain C and resid 28:51)
23X-RAY DIFFRACTION23(chain C and resid 52:82)
24X-RAY DIFFRACTION24(chain C and resid 83:97)
25X-RAY DIFFRACTION25(chain C and resid 98:138)
26X-RAY DIFFRACTION26(chain C and resid 139:159)
27X-RAY DIFFRACTION27(chain C and resid 160:210)
28X-RAY DIFFRACTION28(chain C and resid 211:276)
29X-RAY DIFFRACTION29(chain C and resid 277:303)
30X-RAY DIFFRACTION30(chain C and resid 304:326)
31X-RAY DIFFRACTION31(chain D and resid 2:27)
32X-RAY DIFFRACTION32(chain D and resid 28:51)
33X-RAY DIFFRACTION33(chain D and resid 52:97)
34X-RAY DIFFRACTION34(chain D and resid 98:137)
35X-RAY DIFFRACTION35(chain D and resid 138:161)
36X-RAY DIFFRACTION36(chain D and resid 162:196)
37X-RAY DIFFRACTION37(chain D and resid 197:225)
38X-RAY DIFFRACTION38(chain D and resid 226:284)
39X-RAY DIFFRACTION39(chain D and resid 285:320)
40X-RAY DIFFRACTION40(chain D and resid 321:326)

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