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- PDB-4eg2: 2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 4eg2
Title2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine
ComponentsCytidine deaminase
KeywordsHYDROLASE / Cytidine deaminase / UMP synthesis / ZN binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


pyrimidine-containing compound salvage / cytidine deaminase / cytidine deamination / cytidine deaminase activity / zinc ion binding / cytosol
Similarity search - Function
Cytidine deaminase, bacteria / Cytidine deaminase, homodimeric / Cytidine/deoxycytidylate deaminase, zinc-binding domain / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain ...Cytidine deaminase, bacteria / Cytidine deaminase, homodimeric / Cytidine/deoxycytidylate deaminase, zinc-binding domain / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / URIDINE / Cytidine deaminase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Wang, Y. / Grimshaw, S. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Wang, Y. / Grimshaw, S. / Papazisi, L. / Savchenko, A. / Anderson, W.F.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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
Revision 1.3Dec 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

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Assembly

Deposited unit
A: Cytidine deaminase
B: Cytidine deaminase
C: Cytidine deaminase
D: Cytidine deaminase
E: Cytidine deaminase
F: Cytidine deaminase
G: Cytidine deaminase
H: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,17934
Polymers262,1478
Non-polymers3,03326
Water23,7261317
1
A: Cytidine deaminase
B: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2989
Polymers65,5372
Non-polymers7627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-103 kcal/mol
Surface area21300 Å2
MethodPISA
2
C: Cytidine deaminase
D: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2748
Polymers65,5372
Non-polymers7376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-97 kcal/mol
Surface area21920 Å2
MethodPISA
3
E: Cytidine deaminase
F: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,39210
Polymers65,5372
Non-polymers8558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-98 kcal/mol
Surface area21410 Å2
MethodPISA
4
G: Cytidine deaminase
H: Cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2157
Polymers65,5372
Non-polymers6785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-96 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.810, 163.730, 111.950
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Cytidine deaminase / / Cytidine aminohydrolase / CDA


Mass: 32768.363 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: cdd, VC_1231 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9KSM5, cytidine deaminase

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Non-polymers , 5 types, 1343 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-URI / URIDINE / Uridine


Mass: 244.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H12N2O6
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1317 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES. Screen solution: 0.2M MgCl2, 0.1M Hepes, 10mM Cytidine, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97959 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2011 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.2→41 Å / Num. obs: 116604 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.07 / Num. unique all: 16892 / % possible all: 92.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CTU
Resolution: 2.2→40.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.981 / SU ML: 0.091
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21039 6173 5 %RANDOM
Rwork0.15923 ---
all0.16178 116604 --
obs0.16178 116604 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.353 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å2-0.21 Å2
2--0.07 Å2-0 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18032 0 181 1317 19530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218807
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212352
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9825556
X-RAY DIFFRACTIONr_angle_other_deg0.854330341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.45852410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14725.104819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.404153074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3681583
X-RAY DIFFRACTIONr_chiral_restr0.0820.22883
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02121258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023589
X-RAY DIFFRACTIONr_mcbond_it0.8121.512013
X-RAY DIFFRACTIONr_mcbond_other0.2261.54824
X-RAY DIFFRACTIONr_mcangle_it1.434219171
X-RAY DIFFRACTIONr_scbond_it2.91136794
X-RAY DIFFRACTIONr_scangle_it4.2174.56385
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 449 -
Rwork0.253 8352 -
obs-8352 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)
15.72191.6612-3.54664.0038-4.27610.42510.26310.05170.25530.19630.03350.2916-0.2811-0.662-0.29660.17810.0885-0.06120.16150.02680.1824-15.814347.4549-10.8878
21.786-0.0333-0.50380.48530.12382.09040.11250.20440.056-0.1854-0.02120.0539-0.1495-0.1741-0.09130.11570.0285-0.03640.0320.01210.0626-6.3543.9743-6.7029
31.160.0854-0.20231.02820.04861.37970.0099-0.00320.0574-0.1091-0.031-0.1033-0.13480.0780.02110.07380.0169-0.01980.0154-0.00320.0452.170141.60976.9592
44.06480.2473-0.74763.3468-0.23731.7988-0.15210.1899-0.4663-0.14540.1354-0.02230.24430.07280.01670.17670.0321-0.02580.0389-0.01470.0974-1.447418.05664.1665
52.09970.24080.44111.37340.36651.5401-0.00760.0433-0.0681-0.03180.00720.10470.1656-0.11160.00040.0693-0.0027-0.02190.02080.0060.0409-9.409725.692810.0158
62.6687-0.40460.47132.9147-0.44593.09940.0013-0.1712-0.2230.0955-0.009-0.18990.25960.25940.00760.0830.015-0.03740.17670.00460.057215.205438.96844.9006
71.32850.10280.45581.44550.76411.7520.044-0.10020.0620.1145-0.0295-0.1658-0.00920.1696-0.01450.0304-0.0084-0.01930.07070.01090.038.040443.136533.9208
80.41170.16450.67841.4251-0.6724.81120.0681-0.00050.0635-0.0375-0.1846-0.1768-0.03650.67960.11650.0651-0.01810.00550.13210.01330.18.712850.287122.7069
90.70470.0296-0.0081.5997-0.66592.30010.0396-0.12270.05770.0864-0.01890.1021-0.0019-0.074-0.02080.0163-0.0041-0.00610.0278-0.01950.037-10.397742.45532.5456
102.9237-1.62690.71713.2065-1.32012.60840.1467-0.1632-0.1616-0.0925-0.04940.27560.2434-0.123-0.09720.046-0.0437-0.02430.05420.01710.0396-14.94931.16731.482
111.7698-0.428-1.90841.57161.11963.9086-0.0780.05170.03470.2418-0.0039-0.40060.04770.35190.08190.1972-0.1408-0.03220.322-0.08320.282936.09653.7524-0.1937
121.9479-0.001-0.80581.23140.69063.29770.1306-0.38420.12920.2907-0.0375-0.0809-0.01140.3726-0.0930.1462-0.0895-0.04610.1526-0.03670.097428.282947.79910.1452
131.6546-0.2882-0.35480.89540.19121.81760.0639-0.11890.15130.1144-0.0445-0.0011-0.1230.0632-0.01940.0792-0.0366-0.01190.0242-0.0120.051919.852742.9188-14.768
145.6476-2.8263-0.16774.4718-0.68191.90080.009-0.1912-0.42290.1278-0.0621-0.06580.33710.11990.05310.16450.0078-0.07490.01870.03150.109926.589519.7747-12.8803
152.0844-0.01610.68770.60890.00511.49230.0323-0.0195-0.10020.089-0.0323-0.12980.10270.2648-00.05690.0091-0.04260.06170.01760.052832.493828.783-19.2601
169.1757-3.6202-1.09159.62912.29226.94450.0127-0.0776-0.091-0.11080.1758-0.25420.51320.1343-0.18840.2318-0.0828-0.01620.14270.01720.05535.508229.9844-50.0274
171.0140.25170.89570.912-0.47582.40750.00010.15470.1463-0.0652-0.00010.1829-0.0337-0.07370.00010.03910.0135-0.02120.0850.02190.053810.71642.1871-46.5036
182.6656-0.27240.66620.35071.03414.6432-0.0038-0.05960.22850.0128-0.10150.0864-0.0369-0.58070.10520.13530.00080.01070.11650.02590.237510.736849.7901-31.6546
193.31080.8083-0.2411.6323-0.78444.09390.2537-0.02370.7519-0.01830.02120.0268-0.61440.2213-0.27490.2287-0.11920.03090.14880.0360.291633.662651.7827-40.8275
200.99980.19120.13441.58260.30932.69060.04410.1488-0.0211-0.0254-0.0168-0.0871-0.00010.2533-0.02730.0066-0.0053-0.00470.10640.01360.013432.376939.0393-42.634
2111.51656.7791-1.933315.4476-2.8252.46940.1966-0.30840.43050.2763-0.06430.2699-0.3927-0.2768-0.13230.21110.03470.0730.2595-0.04820.0807-31.869685.359950.6368
221.6681-0.2115-0.49180.92510.1051.5611-0.005-0.1437-0.10960.1670.00050.17210.1237-0.20420.00450.1112-0.0290.01760.0874-0.01510.0628-21.279276.965448.4865
230.7837-0.5709-1.05492.12530.32512.72510.05370.0973-0.1966-0.0682-0.08550.16480.0158-0.41150.03180.1521-0.01740.0060.109-0.01090.155-16.379369.309434.5653
240.9506-0.203-0.62591.36320.99712.87560.0278-0.2196-0.05590.25170.0425-0.13770.08970.1919-0.07030.0847-0.0149-0.03310.0781-0.02310.0753-1.546977.473651.0136
252.5497-0.8744-0.88432.10830.31571.960.0472-0.21310.16380.10570.0396-0.2483-0.19630.3112-0.08680.0868-0.0419-0.02420.1221-0.08810.12333.379787.335649.8213
267.9435-0.09371.65845.2248-1.68965.1321-0.4146-0.7167-0.20680.4893-0.0239-0.5268-0.181-0.150.43860.1468-0.00610.06260.2418-0.06010.351614.633269.78889.9623
271.44020.1064-0.12060.71650.19651.3726-0.03230.157-0.0595-0.13820.0852-0.20180.03830.1149-0.05280.1044-0.02720.05990.0434-0.05230.13011.334877.06815.3212
282.0496-0.7916-1.94343.20983.6224.6873-0.05650.02190.0539-0.0371-0.12360.2130.0207-0.13670.18010.1191-0.00620.00180.0054-0.0090.1337-14.41873.367120.2427
292.83431.48351.45144.4753-0.45582.8186-0.15880.29250.3176-0.17760.0938-0.0213-0.31660.20140.06490.1693-0.04060.06510.0526-0.01220.1574-1.2136101.410120.0252
301.79850.48240.00061.3271-0.39462.0646-0.0245-0.01280.0411-0.01520.042-0.2881-0.21750.2553-0.01750.1181-0.05170.02690.0518-0.0520.14523.925893.078727.7163
315.1258-4.5462-0.50918.95532.34548.7764-0.05820.16020.1927-0.15180.1262-0.1886-0.35430.2452-0.0680.2256-0.12040.02590.207-0.05660.09448.20585.0551-35.881
321.19020.0664-0.80040.70340.30482.58750.00270.0294-0.13660.0112-0.0521-0.08510.38380.07660.04930.2251-0.05490.03060.0712-0.04210.0767-3.948675.0721-27.1857
3330.721412.673810.85845.23254.48173.84032.132-2.902-2.61460.8209-1.2054-1.0730.728-1.0478-0.92661.1537-0.3178-0.07990.68360.08520.5599-20.844863.185-19.6607
340.62610.77120.26792.66890.39642.80660.02560.2664-0.101-0.2336-0.03010.21690.4509-0.83970.00450.2856-0.15770.03670.5652-0.13320.1593-26.363272.5792-40.434
350.65080.1777-0.55191.4722-0.21932.43140.10990.2262-0.0046-0.0427-0.1020.0924-0.0745-0.6142-0.00790.1529-0.07860.01670.3251-0.05890.0526-22.825982.2907-33.233
360.70660.4876-1.24511.5441-0.95512.6172-0.01520.16140.08120.10580.11940.23570.16-0.5541-0.10420.1666-0.1680.03370.2619-0.02350.1742-33.549571.99887.3983
374.98980.06014.04661.61950.83067.6270.04990.0931-0.2637-0.0903-0.02410.03620.3709-0.5643-0.02580.1152-0.1220.06650.1727-0.05740.1028-26.913776.4309-1.2133
381.6592-0.1991-0.41680.472-0.36322.2441-0.0345-0.0562-0.08050.0159-0.0026-0.05720.2707-0.13470.03720.1679-0.10840.04910.081-0.04550.0739-15.933777.5234-4.4129
394.8768-2.89341.26954.5944-0.97112.12280.0092-0.03380.49370.2621-0.0040.1343-0.5148-0.5492-0.00520.42490.06490.14850.299-0.04010.2721-25.7468101.3758-4.103
402.2195-0.4951-0.91991.4963-0.31011.86180.09140.19980.1289-0.00270.05320.315-0.2551-0.6397-0.14460.18180.01230.06790.2823-0.01630.1462-28.920692.0353-11.4026
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 22
2X-RAY DIFFRACTION2A23 - 89
3X-RAY DIFFRACTION3A90 - 172
4X-RAY DIFFRACTION4A173 - 203
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