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- PDB-4bnd: Structure of an atypical alpha-phosphoglucomutase similar to euka... -

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Basic information

Entry
Database: PDB / ID: 4bnd
TitleStructure of an atypical alpha-phosphoglucomutase similar to eukaryotic phosphomannomutases
Components(ALPHA-PHOSPHOGLUCOMUTASE) x 2
KeywordsISOMERASE / SUBSTRATE SPECIFICITY / PHOSPHOGLUCOSE INTERCONVERSION
Function / homology
Function and homology information


phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / phosphatase activity / metal ion binding / cytosol
Similarity search - Function
Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phosphomannomutase / phosphomannomutase
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsNogly, P. / Matias, P.M. / De Rosa, M. / Castro, R. / Santos, H. / Neves, A.R. / Archer, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: High-Resolution Structure of an Atypical [Alpha]-Phosphoglucomutase Related to Eukaryotic Phosphomannomutases
Authors: Nogly, P. / Matias, P.M. / De Rosa, M. / Castro, R. / Santos, H. / Neves, A.R. / Archer, M.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: The Alpha-Phosphoglucomutase of Lactococcus Lactis is Unrelated to the Alpha-D-Phosphohexomutase Superfamily and is Encoded by the Essential Gene Pgmh.
Authors: Neves, A.R. / Pool, W.A. / Castro, R. / Mingote, A. / Santos, F. / Kok, J. / Kuipers, O.P. / Santos, H.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Production and Crystallization of Alpha-Phosphoglucomutase from Lactococcus Lactis.
Authors: Nogly, P. / Castro, R. / De Rosa, M. / Neves, A.R. / Santos, H. / Archer, M.
History
DepositionMay 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Derived calculations
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _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: ALPHA-PHOSPHOGLUCOMUTASE
B: ALPHA-PHOSPHOGLUCOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,54510
Polymers56,8002
Non-polymers7458
Water10,845602
1
B: ALPHA-PHOSPHOGLUCOMUTASE
hetero molecules

A: ALPHA-PHOSPHOGLUCOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,54510
Polymers56,8002
Non-polymers7458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455y-1,x,-z1
Buried area3790 Å2
ΔGint-57.2 kcal/mol
Surface area20740 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-53.5 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.174, 67.174, 210.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8786, -0.1906, 0.4379), (-0.2971, 0.4997, 0.8136), (-0.3739, -0.8449, 0.3824)
Vector: 53.16, 46.29, 53.59)

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Components

#1: Protein ALPHA-PHOSPHOGLUCOMUTASE


Mass: 28429.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363 (lactic acid bacteria)
Plasmid: PNZ8048
Production host: LACTOCOCCUS LACTIS SUBSP. CREMORIS NZ9000 (lactic acid bacteria)
References: UniProt: Q00G41, UniProt: A2RIP9*PLUS, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Protein ALPHA-PHOSPHOGLUCOMUTASE


Mass: 28371.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363 (lactic acid bacteria)
Plasmid: PNZ8048
Production host: LACTOCOCCUS LACTIS SUBSP. CREMORIS NZ9000 (lactic acid bacteria)
References: UniProt: Q00G41, UniProt: A2RIP9*PLUS, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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 % / Description: NONE
Crystal growpH: 7.5
Details: SEEDING, 2.0 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.5→33 Å / Num. obs: 89350 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 8.3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
HKL2MapFOLLOWED BY SHARPphasing
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→30.05 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.329 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 4470 5.08 %RANDOM
Rwork0.1558 ---
obs0.157 89249 99.95 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.3 Å20 Å2
2--0.3 Å20 Å2
3----0.975 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3985 0 46 602 4633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194208
X-RAY DIFFRACTIONr_bond_other_d0.0030.024075
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.9645680
X-RAY DIFFRACTIONr_angle_other_deg0.87339328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12626.698215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83815768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.196157
X-RAY DIFFRACTIONr_chiral_restr0.110.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
X-RAY DIFFRACTIONr_nbd_refined0.2640.21638
X-RAY DIFFRACTIONr_nbd_other0.1820.279
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22071
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9340.5844208
X-RAY DIFFRACTIONr_mcbond_other0.2270.6024074
X-RAY DIFFRACTIONr_mcangle_it1.4340.8535679
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6761.779523
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.8768.8043671
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
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 343 -
Rwork0.244 6175 -
obs--100 %
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)
18.70551.1151-7.55993.25230.011122.3344-0.0175-0.6906-0.23720.5015-0.32930.06350.44750.15240.34670.1088-0.0249-0.01480.19010.04520.106411.92766.0528.736
21.91160.58510.38410.43290.1970.751-0.13180.07610.0031-0.01130.05350.031-0.0610.10990.07840.0905-0.0007-0.0320.12350.03240.120621.3271.516-5.699
31.242-0.7368-0.0992.9153-4.1057.0106-0.0692-0.01850.09930.0277-0.1833-0.22790.01290.30920.25250.07910.0152-0.02070.18910.06020.130331.53570.956-10.711
40.86880.00910.65190.3278-0.33071.51540.05510.0145-0.0595-0.0333-0.02640.00160.09460.1421-0.02870.0850.0515-0.01890.1030.02820.129221.08863.417-8.855
514.5374-1.94370.620116.98769.14138.34560.272-0.3422-0.79180.017-0.28620.26250.48330.01950.01410.16910.0853-0.03240.08070.0470.181216.10351.261-10.662
63.7538-2.57312.812.6828-2.06242.4330.13980.0619-0.177-0.20210.0310.07450.24990.0252-0.17080.10660.0386-0.0240.07720.00370.156710.30860.754-17.019
72.75123.1572-1.16845.5444-2.05851.2548-0.09670.2310.0398-0.15490.07660.0790.01830.04280.02010.0798-0.0137-0.01660.130.0520.112311.03578.597-30.433
83.7877-4.31552.76766.9287-5.30425.09290.09240.13890.20220.0216-0.387-0.2121-0.1260.41470.29460.1077-0.1398-0.0710.25390.1660.208822.6387.78-31.777
94.00960.9372-0.20281.0535-1.04011.6189-0.10070.26330.0316-0.0679-0.0862-0.0045-0.06320.28070.18690.0998-0.0124-0.02090.1890.06620.113123.37976.23-26.867
108.42142.20519.36198.40053.150519.4315-0.29120.5473-0.1902-0.29690.5315-0.0559-0.29670.8186-0.24030.0313-0.0311-0.01140.20960.08410.085631.68375.364-21.274
116.3172-2.34162.586217.9633-2.12841.1398-0.9933-0.07040.6699-0.07660.730.2746-0.3858-0.05910.26320.2464-0.1077-0.13160.33160.15720.18933.11182.324-17.961
1216.5698-12.9354-6.500710.11675.516215.5471-0.674-0.3430.20480.49190.2422-0.1515-0.46060.10790.43180.2176-0.07-0.12840.15640.09890.122226.15989.034-17.867
138.11031.33553.20346.18371.04451.447-0.71590.05560.64340.37350.28160.0268-0.45630.01960.43430.42250.0722-0.29270.18480.04880.271517.64290.299-22.452
1420.97182.002-6.95267.3192-0.78582.3337-0.2562-0.20040.75340.12630.49160.2929-0.00030.008-0.23540.26730.1382-0.09950.21760.07160.16727.98588.815-28.496
1510.66834.88871.65213.8431-0.97692.3967-0.0357-0.01550.28330.09430.08690.075-0.0624-0.105-0.05120.10180.0623-0.03710.07750.02280.14279.75882.723-21.679
160.7990.0939-0.10190.17-0.4911.4711-0.05440.0430.02490.0548-0.0224-0.0079-0.19010.07740.07680.11120.0178-0.030.10130.02550.157612.31477.706-16.137
172.07291.01661.02741.0955-0.09861.1689-0.1081-0.09970.1511-0.0294-0.01020.0966-0.0631-0.04720.11830.08670.031-0.02330.09970.01410.135210.78574.472-3.516
180.9680.53040.53430.34770.09021.2092-0.0936-0.14560.1534-0.0371-0.0680.0759-0.14920.03260.16170.1090.0063-0.03410.13050.01480.151519.48377.92-0.651
190.81681.72010.49394.648-0.94094.3795-0.06170.049-0.0289-0.04170.0968-0.0426-0.07210.109-0.03510.09370.0057-0.03030.13450.02560.124128.26474.0091.341
202.19051.1701-1.0364.7741.20517.66640.04980.0366-0.11250.2528-0.0067-0.08170.3176-0.0395-0.04310.12810.0076-0.05150.09710.03390.118826.76666.4619.698
2133.09734.2941-4.656247.92023.73681.3213-1.45910.4113-2.48610.72860.94560.70890.5827-0.41070.51360.5195-0.4185-0.01090.7342-0.1480.4934-25.61456.738-19.455
222.89861.23861.57711.978-0.00281.3691-0.0432-0.0519-0.079-0.08790.1069-0.09870.006-0.131-0.06370.09610.0092-0.01090.12130.03130.1194-12.47668.877-15.67
232.0179-2.67310.65446.9581-1.00041.1289-0.1451-0.04690.05020.07140.1805-0.12460.00080.0166-0.03550.0790.0329-0.02230.08260.01710.1384-2.1970.165-14.606
242.22841.52721.73233.25650.97161.65910.069-0.0374-0.0572-0.1647-0.0355-0.17780.1705-0.0722-0.03340.13970.0033-0.01110.10250.01010.1372-7.5859.04-17.751
2514.1261-5.87270.046815.1386-0.88810.14760.06880.2869-0.586-0.55030.06450.60770.1169-0.0839-0.13320.1824-0.072-0.10070.13470.04250.1719-15.73955.994-22.857
260.8102-0.1719-0.46912.3257-0.98081.1544-0.07610.05010.0236-0.10.0694-0.11250.16780.01720.00670.11230.0264-0.00840.09520.00480.1158-7.37668.65-24.371
270.2627-0.81280.18352.9023-0.26831.52830.0138-0.00540.0108-0.13240.144-0.01770.1042-0.2363-0.15780.1051-0.0389-0.0180.15960.04670.1178-15.12776.209-31.286
284.26882.98824.06733.1911.68525.7912-0.42720.00950.1924-0.07990.2497-0.1785-0.5111-0.29380.17740.24560.1513-0.07840.1444-0.00610.2812-11.82897.869-16.705
298.0123-5.6058-4.703511.82468.46679.92850.0316-0.15720.39610.16880.4326-0.8029-0.18420.3434-0.46430.0606-0.0121-0.0790.02450.00060.2313.00792.563-15.324
301.2595-0.42830.86540.5539-0.15541.8709-0.05510.00520.08440.02510.1022-0.1332-0.1151-0.0609-0.04710.09680.0497-0.01680.06790.01230.1589-5.66386.278-17.683
3110.9616-3.53050.43993.2506-1.15382.879-0.2922-0.37170.18150.48750.3268-0.2144-0.258-0.2955-0.03460.19990.1486-0.03780.1255-0.01150.0744-9.39987.725-4.218
322.8674-1.45570.813611.3918-1.05591.6782-0.0167-0.32970.09590.19850.2236-0.0954-0.1623-0.6518-0.2070.18610.14040.01160.30270.05820.0868-16.48392.935-9.197
338.39821.84073.451720.7434-0.634615.2689-0.18140.33460.35140.77740.29540.4747-0.2693-0.6911-0.11390.20850.0228-0.05170.35520.10130.1614-20.31398.508-14.808
342.9599-1.50481.46951.6267-0.77191.3639-0.1023-0.12220.04540.12040.20550.0149-0.1235-0.2124-0.10320.11330.10790.01280.12940.05640.1212-17.84788.363-17.403
351.3789-0.00350.5373.98010.61320.44690.0143-0.0975-0.00030.0630.08430.11560.0231-0.2164-0.09860.0986-0.0236-0.00620.27470.13940.1414-24.44275.637-24.18
361.14650.01360.61090.80540.07314.60810.0273-0.0424-0.1241-0.05220.14150.06960.1185-0.1533-0.16880.0816-0.065-0.04870.12170.06840.1094-24.94964.539-20.407
3710.2997-7.9225-2.071412.99382.71843.306-0.26970.04410.17140.30530.26570.04240.0133-0.21820.0040.10390.0506-0.01890.12950.06690.1027-19.43675.066-7.478
381.6818-0.56121.00460.7521-0.48771.3562-0.01290.00220.06850.06620.0971-0.02630.0531-0.2053-0.08430.07510.0023-0.01430.14030.06260.1208-21.3471.779-10.62
390.65810.67680.05673.41171.04310.8438-0.01920.073-0.0134-0.01180.0358-0.07990.08050.0431-0.01660.1060.0132-0.02770.09770.02250.1327-10.97159.309-9.203
4011.0732-8.7751-0.413819.02311.629317.7819-0.11650.4929-0.055-0.57190.20220.59170.58260.8754-0.08560.25150.0008-0.10390.1464-0.00650.145-15.25147.456-12.758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 3
2X-RAY DIFFRACTION2A4 - 14
3X-RAY DIFFRACTION3A15 - 23
4X-RAY DIFFRACTION4A24 - 77
5X-RAY DIFFRACTION5A78 - 82
6X-RAY DIFFRACTION6A83 - 90
7X-RAY DIFFRACTION7A91 - 107
8X-RAY DIFFRACTION8A108 - 115
9X-RAY DIFFRACTION9A116 - 139
10X-RAY DIFFRACTION10A140 - 143
11X-RAY DIFFRACTION11A144 - 148
12X-RAY DIFFRACTION12A149 - 153
13X-RAY DIFFRACTION13A154 - 164
14X-RAY DIFFRACTION14A165 - 168
15X-RAY DIFFRACTION15A169 - 174
16X-RAY DIFFRACTION16A175 - 193
17X-RAY DIFFRACTION17A194 - 225
18X-RAY DIFFRACTION18A226 - 236
19X-RAY DIFFRACTION19A237 - 243
20X-RAY DIFFRACTION20A244 - 251
21X-RAY DIFFRACTION21B0 - 3
22X-RAY DIFFRACTION22B4 - 15
23X-RAY DIFFRACTION23B16 - 23
24X-RAY DIFFRACTION24B24 - 32
25X-RAY DIFFRACTION25B33 - 36
26X-RAY DIFFRACTION26B37 - 65
27X-RAY DIFFRACTION27B66 - 96
28X-RAY DIFFRACTION28B97 - 113
29X-RAY DIFFRACTION29B114 - 121
30X-RAY DIFFRACTION30B122 - 147
31X-RAY DIFFRACTION31B148 - 155
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