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- PDB-5vgc: Crystal structure of the NleG5-1 effector (C200A) from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 5vgc
TitleCrystal structure of the NleG5-1 effector (C200A) from Escherichia coli O157:H7 str. Sakai
ComponentsNleG5-1 effector
KeywordsPROTEIN BINDING / ubiquitination / effectors / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


biological process involved in symbiotic interaction / ubiquitin-protein transferase activity / metal ion binding
Similarity search - Function
Effector protein NleG / Effector protein NleG / Effector protein NleG superfamily / Effector protein NleG / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DUF1076 domain-containing protein
Similarity search - Component
Biological speciesEnterobacteria phage YYZ-2008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBorek, D. / Valleau, D. / Skarina, T. / Jobin, M.C. / Wawrzak, Z. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Contract No. HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of the NleG5-1 effector (C200A) from Escherichia coli O157:H7 str. Sakai
Authors: Valleau, D. / Little, D. / Borek, D. / Skarina, T. / Quaile, A.T. / Di Leo, R. / Houliston, S. / Lemak, A. / Arrowsmith, C. / Combes, B. / Savchenko, A.
History
DepositionApr 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_ncs_dom_lim
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NleG5-1 effector
B: NleG5-1 effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,86413
Polymers48,2812
Non-polymers58311
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-80 kcal/mol
Surface area24710 Å2
2
A: NleG5-1 effector
B: NleG5-1 effector
hetero molecules

A: NleG5-1 effector
B: NleG5-1 effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,72826
Polymers96,5624
Non-polymers1,16622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area12650 Å2
ΔGint-185 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.376, 151.376, 87.983
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 3 - 213 / Label seq-ID: 4 - 214

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein NleG5-1 effector


Mass: 24140.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage YYZ-2008 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: B6DZC0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 20% P3350, 0.2 M CaCl2, 2% Hexanediol, 20 mM Tris pH 9.0, 0.2 M NaCl, 0.3 M KCl2

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Rayonix MX-300
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.55→50.01 Å / Num. obs: 19632 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rsym value: 0.046 / Χ2: 0.875 / Net I/σ(I): 36.38
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 962 / CC1/2: 0.494 / Rpim(I) all: 0.638 / Χ2: 0.887 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KKY
Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.859 / SU B: 24.938 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.88 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29704 1739 10 %RANDOM
Rwork0.24474 ---
obs0.25015 15593 92.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.011 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 26 68 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193367
X-RAY DIFFRACTIONr_bond_other_d0.0010.023137
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9794555
X-RAY DIFFRACTIONr_angle_other_deg0.96537292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24824.848165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74515614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4361526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
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_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_it15.883.0421672
X-RAY DIFFRACTIONr_mcbond_other15.8833.0431671
X-RAY DIFFRACTIONr_mcangle_it23.8964.4992090
X-RAY DIFFRACTIONr_mcangle_other23.894.4992091
X-RAY DIFFRACTIONr_scbond_it12.192.9741694
X-RAY DIFFRACTIONr_scbond_other12.1482.9751694
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.3864.3782465
X-RAY DIFFRACTIONr_long_range_B_refined29.17436.3153840
X-RAY DIFFRACTIONr_long_range_B_other29.17136.3363841
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11632 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 52 -
Rwork0.295 445 -
obs--36.68 %
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)
10.7843-1.8722-3.9944.61949.825221.18770.41880.24450.0824-0.5888-0.6759-0.052-1.158-1.92190.25711.4594-0.43340.69141.0457-0.61161.222-60.203952.94330.6661
29.6858.4514-5.568726.7566-24.855937.1215-0.0482-0.9540.07340.88030.21660.4601-0.1796-0.8264-0.16840.2330.03410.05970.3812-0.22380.3446-53.878250.141229.4848
31.2239-1.64350.83019.9911-3.78371.51020.16260.3587-0.45021.30230.10750.4409-0.358-0.1267-0.27010.6422-0.13210.02071.0941-0.17030.5266-63.056438.69233.1876
410.798410.87714.235864.67387.68051.88970.3623-0.5554-0.762.1591-0.0519-0.26460.259-0.2124-0.31040.3967-0.03410.14150.4089-0.01540.3875-68.336441.116827.7604
56.6951-0.41573.4506111.420310.16949.0921-0.2273-0.01980.7144-4.0322-0.05721.7585-1.351-0.77650.28450.37440.08980.13420.4770.02030.4635-66.976145.911823.4282
62.59340.1877-3.16357.85126.28929.3102-0.5297-0.01720.1591-0.192-0.28611.37640.5679-0.25390.81580.3156-0.2472-0.19940.4277-0.01330.8029-62.295835.223420.9917
728.432123.2586-9.26619.6646-8.78145.28820.4187-0.2090.24790.152-0.745-0.01380.29361.13630.32630.86460.0593-0.02870.7357-0.05560.8366-67.780554.916414.3486
813.7129-8.70894.841214.7301-3.616122.6091-0.08270.36440.9906-0.65120.12711.0899-1.2166-1.3373-0.04440.2055-0.0374-0.05870.29380.01240.4585-58.611548.297719.0554
915.91123.81121.63811.1838-0.24972.48230.2531-0.57910.02270.5955-0.42590.21330.1044-0.64160.17280.0751-0.06520.02120.1912-0.05960.0803-53.787437.979321.7095
101.5232-2.70890.070921.36489.18965.2705-0.1336-0.198-0.35580.32540.22550.51690.1236-0.0954-0.09190.3511-0.10380.08440.1188-0.05440.2302-54.621730.547312.341
116.44012.02434.91194.26254.91116.95690.14330.0912-0.39970.199-0.55290.51430.149-0.45520.40960.2315-0.0844-0.08830.1144-0.08750.2934-52.759819.34723.425
1215.679710.929110.401812.298414.432218.9028-0.65930.58790.287-0.85870.3934-0.1159-0.90930.69510.26590.1425-0.05070.11160.22580.17990.35-53.423115.6244-13.0266
1310.7392.98715.10582.98020.89979.9767-0.45060.7505-0.5788-0.89260.3774-0.2030.3920.69530.07320.3269-0.04760.02880.1345-0.09130.1325-65.43353.4487-22.9077
147.63681.5533-0.092437.385416.67097.51790.34380.3435-0.79960.0572-0.71980.6804-0.0128-0.35090.37610.2251-0.0539-0.05080.193-0.03610.1985-72.2633-2.3569-14.0968
151.327-2.32283.00527.3408-1.764610.5409-0.05910.19890.1381-0.0472-0.2529-0.2393-0.27590.55290.3120.0271-0.0172-0.00780.03380.02120.0145-64.34723.5213-10.471
163.86212.2291-1.042712.97492.64659.3769-0.0403-0.1491-0.0068-0.5569-0.2647-0.2713-0.1125-0.18430.30510.0705-0.0402-0.01210.06570.02390.0378-64.966610.3908-11.0778
173.18162.07521.605115.11490.7980.81480.1166-0.1409-0.01740.1012-0.1060.20280.0539-0.0717-0.01060.1369-0.04170.03030.0255-0.02170.0313-61.418512.3314-2.6415
182.89363.26843.10173.70043.50763.32790.15470.0924-0.19090.25280.0775-0.21710.21930.116-0.23220.24620.03060.00280.22210.05470.0791-55.62127.4399-3.6495
193.18371.463-0.392911.00372.75730.8921-0.25130.3861-0.3058-0.44210.4487-0.9182-0.01980.0774-0.19740.24780.2084-0.02390.3354-0.14010.1121-57.3579-0.0624-16.5767
2019.218310.148-0.0221.9174-5.691620.893-0.29390.2408-1.6774-1.0935-0.2222-1.30161.470.36950.51620.40180.0917-0.08110.027-0.0410.2492-61.5933-9.4914-12.9893
2115.704726.267-4.181848.2575-2.78055.2784-0.1607-1.2938-1.4265-0.2416-1.6022-1.06830.26030.83211.76290.8375-0.12430.15741.12990.12340.8587-24.944710.1096-17.2928
2231.0894.66795.995413.19752.800316.13970.13060.42260.5570.34130.8711-0.6164-0.13261.0023-1.00170.47440.03380.09380.5242-0.02710.4354-26.707617.927-17.2971
232.6102-2.473-6.60722.36026.269316.784-0.0646-0.0396-0.08970.165200.03410.22420.25890.06460.9318-0.056-0.03480.7624-0.19310.746-36.87185.3275-16.9468
246.3246-1.95530.19082.113-3.60818.93070.2934-0.9416-0.9689-0.16810.54630.71710.2626-1.2693-0.83970.8758-0.04650.19530.9343-0.08871.0643-36.74840.8853-6.3857
2527.099229.19066.763831.49017.33251.73870.5765-0.88440.86660.7642-0.71980.84370.341-0.0120.14341.23780.48470.13361.7092-0.04461.0061-23.35476.9131-9.0244
2617.0139-8.8658-7.67529.3754-1.575710.5172-0.583-1.5491-1.42290.3607-0.1677-0.06090.33881.92790.75070.65270.1069-0.22640.54150.07521.5426-36.98989.3251-1.9649
2715.770726.9935-9.791449.2486-17.42376.2437-0.45250.0727-0.7999-1.074-0.1764-1.33180.31550.06340.62880.8646-0.0818-0.09240.86120.02851.1545-16.812813.0908-1.413
28125.511643.198512.52414.87564.28971.3357-0.32462.2122-4.1849-0.08720.6561-1.45230.03430.6371-0.33150.7020.21830.2562.5041-0.39271.4286-25.135717.2964-5.9235
2910.2155-4.9059-4.77878.34534.771512.5937-0.1337-0.7904-0.00470.20970.3199-0.60930.66071.9991-0.18620.2437-0.00860.01570.4483-0.08130.2892-42.10618.72530.4204
304.3034-4.67315.290418.0139-2.59237.27960.41830.1493-0.65350.85430.7014-0.68780.81670.4207-1.11970.6930.0628-0.04950.44230.01490.4186-48.104126.409824.3945
312.6582-2.2172-7.06432.15276.391419.6187-0.0566-0.60160.17790.74490.521-0.16011.29381.5019-0.46441.7014-0.0592-0.25281.04520.13730.5467-43.896124.425636.9822
3212.86354.84812.12582.37512.01863.080.23960.10040.49740.37590.03630.00640.5740.0625-0.27590.86520.101-0.06130.6897-0.03110.811-35.656618.6846.5748
3344.0786-7.420114.723717.90888.704520.885-0.2733-0.4632-0.7260.9833-0.4868-1.00070.0881-0.62520.76010.5305-0.0832-0.02750.44330.0240.5454-36.04556.28339.5847
3421.6677-3.6037-5.337215.91530.27421.3998-0.52531.13560.86180.24270.6812-0.27060.1478-0.0949-0.15580.8960.0023-0.08840.91180.21890.5085-38.414513.067741.5993
350.8388-2.5286-4.1117.87980.57534.29850.0389-0.09040.10130.62030.7718-0.0588-0.44930.2084-0.81080.80280.118-0.02720.89180.01660.8981-53.1018.934339.3312
365.5532-2.99921.45857.26335.74717.963-0.3441-0.075-0.84660.83570.38170.54260.64310.3421-0.03751.0702-0.1745-0.02440.92220.34131.1229-38.722313.65437.4814
378.6027-13.3598-8.746329.819921.847416.45520.58340.4012-1.1552.4129-1.57071.4142.4009-1.22380.98731.9864-0.5889-0.33330.8570.35770.9497-42.076315.443227.5807
385.8212-10.644118.3194102.8111-36.305660.09710.12330.8811-0.797-2.76661.32314.20521.97010.9541-1.44641.6176-0.90590.84411.7087-0.53991.4032-49.315710.428230.0566
3915.60056.3295-4.660711.99592.84833.77720.0128-2.3882-1.1681.4118-0.5344-0.17520.73750.94060.52161.15090.1719-0.10280.84820.19980.7424-48.795814.917545.4134
4021.6196-2.0972-1.302221.1651-0.06611.0154-0.8643-0.42050.24070.17930.239-0.36510.2352-0.47620.62521.45430.19180.20450.98340.17250.9172-50.5076.365749.6039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 10
2X-RAY DIFFRACTION2A11 - 22
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