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- PDB-1oh8: THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH AN UNPA... -

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Basic information

Entry
Database: PDB / ID: 1oh8
TitleTHE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH AN UNPAIRED THYMIDINE
Components
  • 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP* TP*AP*T)-3'
  • 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*CP*TP*TP*GP*GP*CP* AP*GP*CP*T)-3'
  • DNA MISMATCH REPAIR PROTEIN MUTS
KeywordsDNA BINDING / MISMATCH RECOGNITION / ATP-BINDING
Function / homology
Function and homology information


adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal ...MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / MutS, DNA mismatch repair protein, domain I / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNatrajan, G. / Lamers, M.H. / Enzlin, J.H. / Winterwerp, H.H.K. / Perrakis, A. / Sixma, T.K.
Citation
Journal: Nucleic Acids Res. / Year: 2003
Title: Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates
Authors: Natrajan, G. / Lamers, M.H. / Enzlin, J.H. / Winterwerp, H.H.K. / Perrakis, A. / Sixma, T.K.
#1: Journal: Nature / Year: 2000
Title: The Crystal Structure of DNA Mismatch Repair Protein Muts Binding to a G X T Mismatch
Authors: Lamers, M.H. / Perrakis, A. / Enzlin, J.H. / Winterwerp, H.H. / De Wind, N. / Sixma, T.K.
History
DepositionMay 23, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Derived calculations / Other / Source and taxonomy
Category: pdbx_database_status / pdbx_entity_src_syn ...pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _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.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_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_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
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
E: 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP* TP*AP*T)-3'
F: 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*CP*TP*TP*GP*GP*CP* AP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,4146
Polymers197,9634
Non-polymers4522
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-88.7 kcal/mol
Surface area69180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.381, 91.719, 259.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA MISMATCH REPAIR PROTEIN MUTS / / MUTS / FDV / B2733


Mass: 89604.359 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: B834 DE3 / Variant: PLYSS / Plasmid: PM800 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 DE3 / Variant (production host): PLYSS / References: UniProt: P23909

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP* TP*AP*T)-3'


Mass: 9184.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP *GP*AP*CP*AP*CP*TP*GP*GP*TP*GP*CP*CP*TP*TP*GP*GP*CP* AP*GP*CP*T)-3'


Mass: 9569.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 139 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT CARRIES OUT THE MISMATCH ...THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT CARRIES OUT THE MISMATCH RECOGNITION STEP. THIS PROTEIN HAS A WEAK ATPASE ACTIVITY. BELONGS TO THE DNA MISMATCH REPAIR MUTS FAMILY.

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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: 2.6 Å3/Da / Density % sol: 52.2 %
Description: STRUCTURE DETERMINED BY RIGID BODY REFINEMENT USING REFMAC5
Crystal growpH: 7
Details: 12-14 % PEG 6000, 150-300 MM NACL 25 MM HEPES PH 7-8, 10 MM MGCL2, 100-150 MICROM ADP
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111-14 %PEG60001reservoir
2350-750 mM1reservoirNaCl
310 mM1reservoirMgCl2
425 mMHEPES1reservoirpH7.5
514 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2001 / Details: MIRRORS
RadiationMonochromator: GE 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 47871 / % possible obs: 98.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.54
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.2 / % possible all: 92.4
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å / Num. obs: 48882 / Num. measured all: 332212 / Rmerge(I) obs: 0.124
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 92.4 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.57

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3M
Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.867 / SU B: 20.82 / SU ML: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2360 5 %RANDOM
Rwork0.217 ---
obs0.221 44850 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å20 Å20 Å2
2--8.2 Å20 Å2
3----4.21 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12171 569 28 137 12905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113046
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211888
X-RAY DIFFRACTIONr_angle_refined_deg1.2592.0317773
X-RAY DIFFRACTIONr_angle_other_deg0.817327571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27651536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.21991
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214072
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022510
X-RAY DIFFRACTIONr_nbd_refined0.2120.23011
X-RAY DIFFRACTIONr_nbd_other0.2220.214508
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.28238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3251.57676
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.631212329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.91735370
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6354.55444
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: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.397 160
Rwork0.304 3021
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)
13.4840.22670.99213.665-0.72573.74560.0621-0.25740.26180.1912-0.01740.21460.0294-0.3318-0.04470.34550.0210.0180.35690.04650.37996.543635.598233.8174
22.71370.9993-0.3152.81770.29442.54610.0190.2035-0.0161-0.1514-0.01730.0969-0.04830.1975-0.00180.26590.036-0.030.11480.0280.353232.054436.755118.9152
31.2817-0.5271-0.95921.14390.88052.3218-0.0373-0.6198-0.37030.10770.0791-0.1540.27460.3658-0.04180.36080.0462-0.01830.4920.080.438545.787624.601932.8701
43.13983.2308-6.6104-6.94871.7580.3382-0.548-0.9721-0.49460.15330.7144-0.0190.19941.0373-0.16640.52950.2727-0.0990.59830.19660.371353.477617.578632.2146
55.97493.3832-2.47929.47690.82419.32250.1683-0.0619-0.1324-0.15930.2014-0.2629-0.50450.6489-0.36970.48650.0650.02940.4344-0.03040.2062.722128.962776.5737
66.1034-1.0222-3.88751.93030.86565.43120.0224-1.1590.04930.52330.1480.1954-0.12920.7767-0.17040.5273-0.0174-0.03220.71490.03790.340436.859536.739853.9881
71.9619-0.1883-2.4161-0.32580.1582.48340.34860.10640.34620.2098-0.06540.0459-0.1643-0.4237-0.28310.5173-0.12850.07240.8126-0.06880.505226.809241.010254.7658
81.41160.72081.05912.04842.09174.9797-0.0861-0.0764-0.28330.1020.161-0.10090.2159-0.1767-0.07490.24340.0080.10710.17450.02470.594151.032611.76055.4581
99.10599.1371-7.814-4.9808-4.538518.00820.2501-1.021-1.55220.1816-0.5477-0.51091.50420.3250.29760.49410.17170.04970.23030.04691.071254.4208-5.31085.9301
1010.98541.86370.03847.1762-3.07149.7302-0.3554-0.5592-0.69660.04610.1762-0.9789-0.09640.02110.17920.28290.1634-0.06040.0947-0.04790.664244.1974-13.8668-5.1315
119.1167.0803-6.244412.1004-0.678112.24521.2048-1.10450.86791.3806-0.3907-0.351-1.85121.3889-0.81420.9386-0.35030.07190.6704-0.10640.717416.67891.944443.6416
124.2066-0.1832-2.27243.99521.03364.1009-0.06350.1306-0.1350.06610.219-0.44590.28910.4945-0.15550.4177-0.0342-0.03520.29770.00810.343312.5011-18.616725.8903
132.8751-0.0684-2.72640.9348-0.16774.44880.2336-0.02590.159-0.0359-0.08410.0154-0.1387-0.2269-0.14960.380.0757-0.00550.28360.11990.351-2.0491-5.611413.5211
14-1.25981.3418-4.74213.5012-4.30198.0348-0.2657-0.10050.17020.16030.6501-0.3455-0.5323-2.1073-0.38440.33660.13850.03310.56420.19660.291-3.6298-2.45273.7624
156.79333.58-2.324113.21452.46271.0002-0.13220.30590.3824-0.5057-0.43451.0228-0.8081-0.92770.56660.70430.2494-0.16060.9786-0.10140.4564-17.216727.145961.1869
164.2371-2.7996-2.51064.58446.81210.31570.2681-0.08930.3970.0082-0.4438-0.0459-0.1691-1.41950.17570.437-0.13450.03410.63020.15160.4013-18.9378-2.287533.3452
171.0886-0.0170.97840.3493-0.8303-2.1543-0.2036-0.5475-0.06230.4091-0.2180.52530.0063-0.15660.42160.6486-0.12640.08130.66320.00940.42-16.0097-1.709143.5335
188.0781-0.5441-0.60861.0314-0.40581.0301-0.00360.0181-0.231-0.03440.0875-0.0959-0.056-0.0336-0.0840.3120.03510.0490.12920.05180.326520.8904-8.4553-6.9806
192.81790.6673028.4638-1.42040.3076-0.28520.08871.20230.26650.86431.1478-0.19360.0223-0.57910.39010.02150.0480.41540.02650.468822.6576.2775-16.4523
205.82393.67835.46686.93841.79882.7874-0.5923-0.0182-0.0279-0.6890.5384-0.3005-0.36490.35740.05390.38060.06650.14890.20520.06290.419939.767211.5205-16.1998
212.65562.3941-2.9352-2.0447-1.4877.9075-0.0004-0.1516-0.08960.44680.24380.2210.1509-0.4068-0.24340.732-0.05650.04660.5783-0.12410.5878-0.580127.035551.3749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 115
2X-RAY DIFFRACTION2A116 - 265
3X-RAY DIFFRACTION3A266 - 387
4X-RAY DIFFRACTION4A550 - 567
5X-RAY DIFFRACTION5A444 - 503
6X-RAY DIFFRACTION6A388 - 443
7X-RAY DIFFRACTION7A504 - 549
8X-RAY DIFFRACTION8A568 - 741
9X-RAY DIFFRACTION8A1801
10X-RAY DIFFRACTION8A1802
11X-RAY DIFFRACTION9A742 - 765
12X-RAY DIFFRACTION10A766 - 800
13X-RAY DIFFRACTION11B2 - 115
14X-RAY DIFFRACTION12B116 - 265
15X-RAY DIFFRACTION13B266 - 387
16X-RAY DIFFRACTION14B550 - 567
17X-RAY DIFFRACTION15B444 - 503
18X-RAY DIFFRACTION16B388 - 443
19X-RAY DIFFRACTION17B504 - 549
20X-RAY DIFFRACTION18B568 - 741
21X-RAY DIFFRACTION19B742 - 765
22X-RAY DIFFRACTION20B766 - 800
23X-RAY DIFFRACTION21E1 - 14
24X-RAY DIFFRACTION21F17 - 30
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.261

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  • 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

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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

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