[English] 日本語
Yorodumi
- PDB-3dc8: Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dc8
TitleCrystal structure of dihydropyrimidinase from Sinorhizobium meliloti
ComponentsDihydropyrimidinase
KeywordsHYDROLASE / TIM-barrel
Function / homology
Function and homology information


dihydropyrimidinase / dihydropyrimidinase activity / metal ion binding / cytoplasm
Similarity search - Function
Hydantoinase/dihydropyrimidinase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Dihydropyrimidinase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Citation
Journal: J.Struct.Biol. / Year: 2010
Title: Structure of dihydropyrimidinase from Sinorhizobium meliloti CECT4114: new features in an amidohydrolase family member
Authors: Martinez-Rodriguez, S. / Martinez-Gomez, A.I. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Garcia-Ruiz, J.M. / Las Heras-Vazquez, F.J. / Gavira, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary crystallographic studies of the recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114
Authors: Martinez-Rodriguez, S. / Gonzalez-Ramirez, L.A. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Las Heras-Vazquez, F.J. / Gavira, J.A. / Garcia-Ruiz, J.M.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 700SHEET Determination method: Author determined

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydropyrimidinase
B: Dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82912
Polymers107,0812
Non-polymers74810
Water24,1041338
1
A: Dihydropyrimidinase
B: Dihydropyrimidinase
hetero molecules

A: Dihydropyrimidinase
B: Dihydropyrimidinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,65824
Polymers214,1624
Non-polymers1,49620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area17440 Å2
ΔGint-374 kcal/mol
Surface area57140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.887, 126.281, 196.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1204-

HOH

-
Components

#1: Protein Dihydropyrimidinase


Mass: 53540.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: CECT4114 / Gene: dhp / Plasmid: pBSK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0PQZ5, dihydropyrimidinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1338 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 4.6
Details: 4.0M sodium formate, 0.1M sodium acetate, pH 4.6, COUNTER-DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 31, 2006 / Details: Montel mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→39.89 Å / Num. obs: 129593 / % possible obs: 98.4 % / Redundancy: 3.47 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.0662 / Net I/σ(I): 13
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 1.83 % / Mean I/σ(I) obs: 3.11 / Num. unique all: 8930 / Rsym value: 0.311 / % possible all: 89.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å39.89 Å
Translation3 Å39.89 Å

-
Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YNY, 1KCX, 1K1D

1yny

1kcx

1k1d


Resolution: 1.85→29.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.398 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The structure was refined also with COOT 0.2 and MolProbity
RfactorNum. reflection% reflectionSelection details
Rfree0.176 6524 5 %RANDOM
Rwork0.148 ---
obs0.149 129519 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7313 0 36 1338 8687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227588
X-RAY DIFFRACTIONr_bond_other_d0.0010.023
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.94610312
X-RAY DIFFRACTIONr_angle_other_deg0.33236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.55984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22623.799329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.217151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851549
X-RAY DIFFRACTIONr_chiral_restr0.1460.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025776
X-RAY DIFFRACTIONr_nbd_refined0.2020.23856
X-RAY DIFFRACTIONr_nbd_other0.1350.23
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.21214
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.258
X-RAY DIFFRACTIONr_mcbond_it0.9181.54973
X-RAY DIFFRACTIONr_mcangle_it1.16827715
X-RAY DIFFRACTIONr_scbond_it2.02133046
X-RAY DIFFRACTIONr_scangle_it2.8354.52582
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 419 -
Rwork0.203 8073 -
all-8492 -
obs--88.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4189-0.2717-0.60421.8312-0.48991.3888-0.19870.37440.0706-0.41990.05210.2142-0.1066-0.08870.1467-0.0603-0.04770.0006-0.01560.0057-0.1311-33.335-9.358-40.951
25.88699.6521-2.42120.5239-4.50635.5912-0.16880.4235-0.4185-0.1115-0.0523-0.90620.33390.07070.2211-0.0823-0.0240.0161-0.0194-0.0527-0.1-28.913-17.173-43.252
31.19780.3549-0.24361.9279-1.18712.0931-0.03120.28690.0464-0.36140.03610.12920.2123-0.1449-0.0049-0.0799-0.0319-0.023-0.0499-0.0451-0.1018-37.843-14.848-34.366
40.6304-0.16150.23921.4574-2.86068.88520.03920.0333-0.0481-0.0188-0.01640.06910.38290.1762-0.0228-0.0871-0.05790.0121-0.0995-0.0337-0.0571-42.861-31.658-15.642
54.6692-1.83791.77841.3248-0.0131.46220.0339-0.2457-0.41090.12660.14980.22420.3372-0.3036-0.1837-0.0574-0.07780.011-0.0763-0.0127-0.0692-34.911-28.954-19.125
64.4155-1.66343.1970.877-0.4434.63030.06520.0327-0.48160.0590.03150.24070.452-0.1475-0.0967-0.0358-0.05790.0338-0.0967-0.0393-0.032-33.187-34.461-22.199
71.8541-1.09061.90356.5514-0.22012.7125-0.1077-0.0592-0.36650.70280.0224-0.13770.5950.1980.08520.0142-0.0075-0.0052-0.1344-0.0334-0.0185-19.01-36.074-12.346
80.9036-0.1242-0.55011.16110.69622.2284-0.0146-0.011-0.11680.1468-0.02320.02980.2622-0.10620.0378-0.0824-0.01510.0098-0.1472-0.0196-0.079-23.099-27.321-7.52
96.21.1181.43880.4687-0.25021.30610.0251-0.28930.00020.1656-0.04350.00130.04-0.18770.0184-0.0568-0.05360.0133-0.0784-0.0243-0.1037-41.515-22.8268.244
1010.35460.4294-3.66580.3578-0.11991.9462-0.0656-0.0260.16760.02110.04070.10490.0411-0.15560.0249-0.0875-0.0251-0.0144-0.1113-0.0076-0.1304-33.121-16.0112.578
113.2336-1.82-0.23551.66250.48061.64260.0021-0.02450.05990.0918-0.0053-0.0390.0321-0.00910.0032-0.1167-0.02930.0036-0.171-0.0018-0.1182-23.5-16.442-5.97
1217.0343.10441.57488.02350.20690.5749-0.3438-0.58990.90490.14650.10230.0596-0.4537-0.17310.2416-0.10890.021-0.0472-0.1203-0.0394-0.1207-24.281-7.389-4.846
131.82940.8612-0.55670.9896-0.21360.6879-0.0295-0.05150.06030.02410.01630.07720.0074-0.10540.0132-0.1174-0.0104-0.0044-0.1049-0.0142-0.113-39.1-12.74-8.425
143.23052.02141.8951.7612.663110.89020.0776-0.089-0.24540.199-0.02130.03260.5439-0.1688-0.0563-0.0931-0.05130.0283-0.129-0.0146-0.0609-50.538-29.064-2.803
150.37760.0984-0.07740.5048-0.20780.5737-0.01190.1032-0.0143-0.04540.00280.07540.0404-0.12990.0091-0.1276-0.0319-0.0061-0.092-0.0219-0.1194-35.09-12.611-24.921
1612.83958.5197-13.18956.5987-13.001332.6478-0.18150.79840.3516-0.25660.85420.49430.4654-1.1813-0.6727-0.10420.002-0.0237-0.01160.0179-0.0458-51.171-8.219-27.458
170.29990.0021-0.64970.8815-0.13911.465-0.01970.145-0.0063-0.02560.01340.14270.0092-0.23170.0063-0.1226-0.041-0.02970.0022-0.0101-0.0834-48.226-17.42-25.198
1810.3664-1.10163.52422.76970.07582.63810.08890.5117-0.0421-0.239-0.08060.18330.0933-0.1008-0.0084-0.0304-0.07560.0232-0.0359-0.0157-0.1462-39.332-26.077-32.47
199.06784.66736.23773.87772.4416.7429-0.15820.103-0.2525-0.00820.1416-0.20530.02160.21920.0166-0.11870.00230.0442-0.1214-0.0146-0.1146-8.995-17.671-16.062
204.8285-4.04564.61276.2827-4.69017.55660.03340.37260.2128-0.1935-0.1333-0.37230.26650.4130.0999-0.10030.071-0.01680.0188-0.0699-0.075910.466-22.2375.737
212.21520.3342-1.84380.3085-0.48145.1603-0.11190.1089-0.1443-0.1744-0.00820.00180.26570.00930.1201-0.0861-0.02050.0223-0.1134-0.0201-0.1282-11.153-10.848-39.27
223.42855.3002-0.646526.7206-3.39613.41250.07490.3614-0.228-0.7624-0.26210.00220.2361-0.06910.1872-0.0775-0.02120.009-0.0553-0.0343-0.1429-14.483-7.386-46.56
230.58670.0407-0.26791.97931.26811.8099-0.00070.0530.003-0.214-0.0395-0.0268-0.09680.06360.0402-0.1167-0.00790.0228-0.10650.0184-0.1403-6.375-0.815-36.19
242.65480.5026-0.89054.66880.57185.93430.055-0.31320.47760.4178-0.0414-0.0412-0.9578-0.2151-0.01360.1319-0.025-0.0158-0.017-0.0060.0252-2.18522.385-27.448
253.4147-1.4129-0.72992.93660.77480.7485-0.0191-0.06750.15580.03190.0492-0.0505-0.14980.066-0.0301-0.1016-0.02110.0158-0.10240.0057-0.1444-6.25310.508-32.004
2636.7344-1.950814.60267.6997-6.571222.4337-1.5245-0.5281.43441.1430.3328-1.0497-3.18090.2331.19170.4011-0.0582-0.1199-0.0820.00430.0278-16.34230.425-26.435
2717.0461-9.137-4.80418.33231.86464.37770.27010.14020.5868-0.5530.0109-0.6149-0.75280.3385-0.2810.0714-0.05810.0197-0.05190.05740.0122-12.56425.499-35.15
282.9178-1.2412-1.38812.61140.81491.39990.01460.1640.26940.03970.00910.0165-0.3405-0.0421-0.02370.010.0117-0.0159-0.10940.0441-0.0719-20.63222.847-30.047
290.554-0.02990.4771.0040.15192.8548-0.01090.02520.1028-0.0157-0.0095-0.0097-0.36550.12020.0204-0.0688-0.0049-0.0023-0.13270.0123-0.0937-22.22221.138-18.973
304.02111.1663-0.06381.39130.09320.01290.0309-0.15570.12030.0813-0.0205-0.0252-0.08980.0635-0.0103-0.0679-0.02950.015-0.099-0.023-0.1264-6.22621.54-3.307
312.8902-0.77240.25151.3912-0.45341.3953-0.0657-0.1425-0.01740.07130.04340.07-0.0124-0.00810.0223-0.1125-0.00360.0193-0.1579-0.013-0.1368-21.36510.14-11.026
321.64971.09290.14271.4588-0.00280.57880.02-0.1283-0.0080.0041-0.0062-0.0805-0.04390.0394-0.0138-0.0981-0.01530.023-0.134-0.0184-0.1405-5.1869.094-12.194
332.01990.79780.31710.65670.71111.2504-0.0596-0.06560.0223-0.00240.0296-0.0517-0.01920.13380.03-0.13160.00050.0119-0.1288-0.0067-0.1056-6.9536.473-13.914
349.93762.82571.21637.71377.936112.9559-0.54140.52290.1611-0.64120.47430.0164-0.41930.12650.0671-0.0491-0.112-0.0111-0.08540.0081-0.12736.34322.203-20.5
354.25111.1889-3.74873.09370.81957.89750.1450.12760.3638-0.25070.05870.1754-0.4525-0.2074-0.2037-0.0898-0.04920.01-0.1110.0172-0.05933.27425.815-12.607
360.5288-0.00450.04590.71270.01120.85120.02030.04170.0253-0.0335-0.0178-0.029-0.03380.0886-0.0025-0.1292-0.02030.019-0.1212-0.0112-0.1421-10.365-0.932-28.324
3731.344429.863513.528431.071816.516110.8611-0.32550.4074-0.1822-0.15110.5944-0.5527-0.04250.3844-0.2689-0.11150.00630.0307-0.068-0.0179-0.10365.33-6.975-29.077
380.38050.2240.33461.05330.42921.28870.03470.09410.0409-0.02130.0497-0.1205-0.0540.2535-0.0844-0.1002-0.02320.0313-0.0588-0.0254-0.09243.5863.989-30.295
394.10560.0075-1.8940.4026-0.25931.48090.07550.3520.0486-0.1096-0.0147-0.043-0.0776-0.1262-0.0608-0.0414-0.036-0.0107-0.1102-0.0225-0.1051-17.079.697-35.051
4030.6477-16.0537-27.268710.50116.088925.8201-0.03030.7913-0.2525-0.3662-0.53340.4079-0.2319-1.10780.5637-0.07450.0112-0.0162-0.0415-0.06880.0661-47.94412.266-12.073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 242 - 24
2X-RAY DIFFRACTION2AA25 - 3125 - 31
3X-RAY DIFFRACTION3AA32 - 6032 - 60
4X-RAY DIFFRACTION4AA61 - 7661 - 76
5X-RAY DIFFRACTION5AA77 - 9977 - 99
6X-RAY DIFFRACTION6AA100 - 121100 - 121
7X-RAY DIFFRACTION7AA122 - 140122 - 140
8X-RAY DIFFRACTION8AA141 - 182141 - 182
9X-RAY DIFFRACTION9AA183 - 206183 - 206
10X-RAY DIFFRACTION10AA207 - 219207 - 219
11X-RAY DIFFRACTION11AA220 - 242220 - 242
12X-RAY DIFFRACTION12AA243 - 249243 - 249
13X-RAY DIFFRACTION13AA250 - 316250 - 316
14X-RAY DIFFRACTION14AA317 - 331317 - 331
15X-RAY DIFFRACTION15AA332 - 394332 - 394
16X-RAY DIFFRACTION16AA395 - 401395 - 401
17X-RAY DIFFRACTION17AA402 - 434402 - 434
18X-RAY DIFFRACTION18AA435 - 452435 - 452
19X-RAY DIFFRACTION19AA453 - 470453 - 470
20X-RAY DIFFRACTION20AA471 - 484471 - 484
21X-RAY DIFFRACTION21BB2 - 232 - 23
22X-RAY DIFFRACTION22BB24 - 3424 - 34
23X-RAY DIFFRACTION23BB35 - 6035 - 60
24X-RAY DIFFRACTION24BB61 - 7461 - 74
25X-RAY DIFFRACTION25BB75 - 9175 - 91
26X-RAY DIFFRACTION26BB92 - 9992 - 99
27X-RAY DIFFRACTION27BB100 - 111100 - 111
28X-RAY DIFFRACTION28BB112 - 140112 - 140
29X-RAY DIFFRACTION29BB141 - 182141 - 182
30X-RAY DIFFRACTION30BB183 - 217183 - 217
31X-RAY DIFFRACTION31BB218 - 249218 - 249
32X-RAY DIFFRACTION32BB250 - 281250 - 281
33X-RAY DIFFRACTION33BB282 - 316282 - 316
34X-RAY DIFFRACTION34BB317 - 322317 - 322
35X-RAY DIFFRACTION35BB323 - 334323 - 334
36X-RAY DIFFRACTION36BB335 - 394335 - 394
37X-RAY DIFFRACTION37BB395 - 399395 - 399
38X-RAY DIFFRACTION38BB400 - 436400 - 436
39X-RAY DIFFRACTION39BB437 - 464437 - 464
40X-RAY DIFFRACTION40BB465 - 477465 - 477

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more