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- PDB-4gze: Crystal structure of 6-phospho-beta-glucosidase from Lactobacillu... -

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Basic information

Entry
Database: PDB / ID: 4gze
TitleCrystal structure of 6-phospho-beta-glucosidase from Lactobacillus plantarum (apo form)
Components6-phospho-beta-glucosidase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / glycoside hydrolase / family 1
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / : / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-phospho-beta-glucosidase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsMichalska, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: GH1-family 6-P-beta-glucosidases from human microbiome lactic acid bacteria.
Authors: Michalska, K. / Tan, K. / Li, H. / Hatzos-Skintges, C. / Bearden, J. / Babnigg, G. / Joachimiak, A.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Sep 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _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: 6-phospho-beta-glucosidase
B: 6-phospho-beta-glucosidase
C: 6-phospho-beta-glucosidase
D: 6-phospho-beta-glucosidase
E: 6-phospho-beta-glucosidase
F: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,13713
Polymers334,8326
Non-polymers3057
Water9,854547
1
A: 6-phospho-beta-glucosidase
B: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7536
Polymers111,6112
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-54 kcal/mol
Surface area33540 Å2
MethodPISA
2
C: 6-phospho-beta-glucosidase
D: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7745
Polymers111,6112
Non-polymers1633
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-41 kcal/mol
Surface area33810 Å2
MethodPISA
3
E: 6-phospho-beta-glucosidase
F: 6-phospho-beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)111,6112
Polymers111,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-17 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.086, 96.086, 289.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
6-phospho-beta-glucosidase


Mass: 55805.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: lp_0440, pbg1 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: F9UU25, 6-phospho-beta-glucosidase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.6 M NaCl, 0.1 M MES/NaOH, 20% PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 24, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.718
111.000K, 1.000H, -L20.282
ReflectionResolution: 2.31→50 Å / Num. all: 130885 / Num. obs: 130353 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.8
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.75 / Num. unique all: 6313 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QOM
Resolution: 2.31→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.819 / SU ML: 0.089 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21338 1248 1 %thin resolution shells
Rwork0.17384 ---
all0.17421 130248 --
obs0.17421 130248 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.569 Å2
Baniso -1Baniso -2Baniso -3
1-25.09 Å20 Å20 Å2
2--25.09 Å20 Å2
3----50.17 Å2
Refinement stepCycle: LAST / Resolution: 2.31→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23021 0 12 547 23580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02223683
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215869
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.92932117
X-RAY DIFFRACTIONr_angle_other_deg0.859338323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42252832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3824.0331262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.466153761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.23215131
X-RAY DIFFRACTIONr_chiral_restr0.0820.23290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025261
X-RAY DIFFRACTIONr_mcbond_it0.4661.514087
X-RAY DIFFRACTIONr_mcbond_other0.1271.55803
X-RAY DIFFRACTIONr_mcangle_it0.805222596
X-RAY DIFFRACTIONr_scbond_it1.49739596
X-RAY DIFFRACTIONr_scangle_it2.194.59521
LS refinement shellResolution: 2.309→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 66 -
Rwork0.21 9004 -
obs--94.66 %
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)
13.07042.4831.74224.54912.32573.53790.045-0.14360.1513-0.1537-0.22290.0862-0.25320.04150.17790.05420.01840.03460.06350.05330.143850.5929-23.463718.871
21.07060.40780.1142.5678-0.16111.37610.03160.1984-0.0316-0.07440.04680.17520.0823-0.0248-0.07840.07980.0452-0.0160.0735-0.03190.142644.3457-36.05049.3456
31.41360.6018-0.06631.8022-0.47410.73080.06090.1818-0.2089-0.1304-0.0449-0.04430.18620.0812-0.0160.13760.0606-0.01820.049-0.04560.15547.5741-47.195719.1891
40.5109-0.3839-0.50591.12240.6911.85650.0110.0139-0.0705-0.0326-0.03880.12030.1912-0.03220.02780.05360.0045-0.01660.0027-0.00360.142340.1194-39.61134.2341
51.30530.095-0.3861.9850.05431.6684-0.0201-0.025-0.1703-0.0108-0.0230.08890.1814-0.04760.04310.05090.0106-0.03670.0167-0.02880.097341.5489-40.325636.8949
64.56562.3942-0.93769.54690.19382.7091-0.12920.15740.1562-0.09350.13620.78830.0265-0.3604-0.0070.01980.0336-0.02760.1459-0.02240.166127.6643-26.280437.943
70.6875-0.33790.25090.383-0.38542.38950.080.1080.1638-0.0706-0.06840.0153-0.15260.0385-0.01160.0843-0.0109-0.00920.0390.00290.199944.5343-18.187525.4945
82.26170.570.70411.81090.28772.44460.01680.11950.0341-0.0792-0.02780.1212-0.2036-0.07580.0110.07150.04640.01670.03820.01960.159942.5347-18.867510.523
92.11641.07580.30082.17180.77151.7966-0.03720.04740.18180.08060.06860.1466-0.02620.041-0.03140.07650.02510.01920.02210.02860.152749.1937-29.135274.5432
105.61291.61510.02146.52871.05413.1273-0.6296-0.10681.36780.06490.31290.3296-0.6644-0.31010.31680.41010.0444-0.05860.2654-0.06490.597652.3819-7.522778.4071
111.69210.8193-0.31031.3969-0.48161.1461-0.0149-0.1075-0.02470.16650.0197-0.13620.03580.2097-0.00490.07840.0203-0.05110.0926-0.02240.170460.6621-28.871576.7806
120.9834-0.35310.61590.7358-0.58451.48910.0112-0.0450.0736-0.0064-0.0254-0.0615-0.15610.24490.01420.0459-0.03620.00430.0819-0.03090.163255.8954-21.395357.0649
130.74640.59010.37061.5186-0.5551.2827-0.03230.01760.1046-0.0744-0.0256-0.1598-0.15590.21130.05790.1196-0.06930.0410.0714-0.06770.212957.1462-20.548951.9634
149.6970.97180.09964.48090.41911.27630.13750.0241-0.11960.2797-0.0319-0.0007-0.5908-0.2566-0.10560.3290.13780.02680.1031-0.07310.183938.735-12.595454.8721
150.96240.1193-0.74030.4839-0.07392.3037-0.0529-0.09780.0690.14140.01280.11940.0043-0.11210.040.06410.0072-0.010.05020.00640.165438.523-31.780865.2283
161.22830.51540.05562.99041.49472.5528-0.0606-0.02020.09850.09610.05510.1313-0.024-0.08020.00550.05760.0456-0.01210.09080.0240.155738.9479-29.38380.2467
173.7532-3.0574-1.84844.47792.57723.21740.20330.11680.0953-0.1607-0.1302-0.0637-0.2637-0.077-0.07310.073-0.0387-0.01550.04840.02880.1147-2.06597.09860.2196
181.8856-0.3470.12931.01880.32361.38380.01260.0453-0.1245-0.16830.0756-0.08620.03680.2001-0.08820.062-0.01570.02690.121-0.02660.14227.9285-1.856552.4773
191.8704-1.11870.16351.8565-0.03480.9685-0.0260.07050.0178-0.13470.0328-0.25470.01770.3069-0.00670.0213-0.01190.03290.2007-0.05430.150518.1781-2.030863.6277
200.8582-0.0614-0.53840.4909-0.38091.5967-0.00490.0031-0.11190.0026-0.0367-0.11990.17220.28990.04160.04670.038-0.00410.0875-0.04430.15288.6469-7.420177.5399
218.6123-3.1276-0.23674.30670.55630.69280.31490.4510.0635-0.3256-0.28510.35540.4278-0.0337-0.02980.38990.0073-0.04210.0505-0.07740.2569-9.5658-15.570577.4794
220.5453-0.24420.67780.2354-0.34274.33780.04010.03020.0086-0.08110.00440.0030.1403-0.0458-0.04450.0392-0.01130.01580.0085-0.01470.1209-6.80131.715470.7238
231.74160.51051.11961.24782.51826.4134-0.1163-0.03480.0015-0.1658-0.10780.2495-0.2636-0.23640.22410.06690.0051-0.03090.03130.00560.1515-14.73375.568964.292
240.93730.6721-0.04670.73190.23052.2038-0.00010.0111-0.0566-0.10850.05860.02550.0258-0.0279-0.05860.0883-0.0023-0.02330.05180.00670.1237-8.40181.952953.7373
253.3516-0.3560.83891.1640.18221.2789-0.07990.07890.37660.08750.0724-0.1436-0.08920.08080.00750.12860.0080.02420.01480.02490.18157.24745.657722.0778
263.01840.0148-0.1841.017-0.02350.86970.019-0.0915-0.08290.0997-0.01440.00020.1142-0.034-0.00460.13290.0175-0.04240.01190.00360.09686.7805-5.99725.9376
274.91772.2588-2.56312.8122-1.82922.4301-0.04590.0246-0.18560.1455-0.0388-0.1590.21020.17280.08460.1250.0595-0.04810.04720.00270.124718.5667-11.074916.3365
280.5272-0.30290.08470.8228-0.70381.61340.0019-0.02130.0090.0362-0.0343-0.12420.01870.13660.03240.04030.0204-0.02160.0223-0.00460.129213.33280.42862.9418
292.1677-0.2554-0.27842.3416-0.79941.53560.01190.06330.0235-0.1173-0.0358-0.24510.07770.250.02390.07220.0231-0.04710.0562-0.02080.079414.6273-0.4168-1.7725
3013.4629-2.09312.7444.7136-1.68812.48540.0157-0.29280.5986-0.0478-0.0078-0.1338-0.2955-0.0561-0.00790.1699-0.0159-0.01960.0157-0.02790.17528.708418.4905-1.9115
310.4971-0.0998-0.06320.67230.70922.24220.02760.02870.12690.0837-0.00490.0494-0.1135-0.1502-0.02260.08150.0288-0.00370.01790.01680.1632-5.35178.19512.2303
320.5970.04640.3111.70830.68443.0698-0.03450.03950.07340.03090.07430.0104-0.2448-0.1078-0.03980.09450.02860.03740.02980.01340.1359-7.38088.371225.8511
330.8259-2.50082.04517.5964-6.17665.0830.13770.0596-0.0147-0.3519-0.0324-0.00970.2540.2244-0.10530.4702-0.08290.0480.6267-0.22230.619347.062252.745672.5712
341.44670.888-0.28911.49140.73380.96460.0568-0.209-0.17060.217-0.0872-0.01930.13680.10060.03030.17750.01620.01830.2232-0.04420.266645.623222.791588.8821
351.67880.08560.38442.57040.2791.51520.0071-0.1781-0.27870.210.0946-0.12960.25070.0712-0.10170.20290.00750.04250.22930.03840.288544.674118.791493.372
361.164-0.10310.01881.28870.14880.97560.0186-0.1447-0.2030.0554-0.02260.01180.267-0.09830.0040.2435-0.03610.02690.18920.06210.295341.006314.75782.3065
371.3475-0.1147-0.5670.7154-0.43981.4091-0.00480.0231-0.265-0.0945-0.06910.0530.2931-0.11470.07390.2234-0.03090.00990.10630.01370.293146.697415.245864.7195
385.30790.079-1.90281.65190.27531.68420.065-0.2369-0.07590.072-0.025-0.45810.10230.4236-0.040.20130.0185-0.0250.1780.09410.275860.366525.689168.0956
390.63870.0869-0.61810.67070.42122.5804-0.0394-0.29640.02450.0647-0.0375-0.1711-0.07150.1530.07690.18050.00840.00250.16360.00420.273652.995235.662978.9667
400.6985-0.17320.6690.4733-0.77613.65870.0172-0.19270.03670.0233-0.0571-0.0588-0.02650.21730.03990.1442-0.03190.02090.2132-0.03080.308851.197435.865287.5074
419.6937-5.73365.82311.5345-1.16036.22780.6155-0.1589-0.73310.2185-0.1566-0.08240.95320.4108-0.45890.4246-0.06350.12340.27120.00470.391853.281710.033940.3955
420.724-0.1363-0.14473.4391-0.88151.06680.0470.1640.0945-0.1361-0.0281-0.097-0.0761-0.1157-0.0190.1767-0.03630.01590.2239-0.00140.282747.386538.373220.3194
431.4958-0.06140.3011.81230.54731.3804-0.00590.17950.0496-0.14-0.05220.3315-0.0633-0.2670.05820.1445-0.0196-0.00290.290.0270.2934.62838.487928.0984
440.86950.02120.47831.04740.3531.4233-0.05290.11560.1016-0.0269-0.0280.1385-0.1104-0.21820.08080.1207-0.03470.02140.13850.02640.265541.692739.950445.8919
456.1989-2.79921.17586.2715-0.94334.29020.0821-0.14940.32050.0885-0.0638-0.444-0.14490.2372-0.01830.1539-0.09060.01910.11810.04240.31461.245442.995251.7602
4616.95717.78637.67416.56923.1443.5248-0.28951.3820.5864-0.020.13450.1668-0.10580.6850.1550.3722-0.04730.09670.1922-0.01190.436764.41529.295342.8333
471.1697-0.0834-1.00370.3708-0.32892.729-0.14150.1859-0.1401-0.01490.0083-0.10550.2494-0.07210.13320.1894-0.06170.04270.076-0.03220.290755.587124.104936.9619
481.570.1209-0.32922.7372-0.45922.5552-0.06980.17830.0594-0.12010.01-0.20430.15370.09270.05980.1507-0.05190.02850.1841-0.02870.252657.531827.041822.4801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 29
2X-RAY DIFFRACTION2A30 - 134
3X-RAY DIFFRACTION3A135 - 176
4X-RAY DIFFRACTION4A177 - 286
5X-RAY DIFFRACTION5A287 - 326
6X-RAY DIFFRACTION6A327 - 343
7X-RAY DIFFRACTION7A344 - 425
8X-RAY DIFFRACTION8A426 - 478
9X-RAY DIFFRACTION9B2 - 45
10X-RAY DIFFRACTION10B46 - 57
11X-RAY DIFFRACTION11B58 - 171
12X-RAY DIFFRACTION12B172 - 282
13X-RAY DIFFRACTION13B283 - 326
14X-RAY DIFFRACTION14B327 - 350
15X-RAY DIFFRACTION15B351 - 425
16X-RAY DIFFRACTION16B426 - 478
17X-RAY DIFFRACTION17C2 - 29
18X-RAY DIFFRACTION18C30 - 137
19X-RAY DIFFRACTION19C138 - 181
20X-RAY DIFFRACTION20C182 - 320
21X-RAY DIFFRACTION21C321 - 350
22X-RAY DIFFRACTION22C351 - 386
23X-RAY DIFFRACTION23C387 - 416
24X-RAY DIFFRACTION24C417 - 478
25X-RAY DIFFRACTION25D0 - 65
26X-RAY DIFFRACTION26D66 - 142
27X-RAY DIFFRACTION27D143 - 171
28X-RAY DIFFRACTION28D172 - 283
29X-RAY DIFFRACTION29D284 - 326
30X-RAY DIFFRACTION30D327 - 343
31X-RAY DIFFRACTION31D344 - 437
32X-RAY DIFFRACTION32D438 - 478
33X-RAY DIFFRACTION33E1 - 6
34X-RAY DIFFRACTION34E7 - 42
35X-RAY DIFFRACTION35E49 - 110
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