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- PDB-1oh7: THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A G:G M... -

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Basic information

Entry
Database: PDB / ID: 1oh7
TitleTHE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A G:G MISMATCH
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*GP*TP*GP*GP *CP*AP*GP*CP*T)-3'
  • DNA MISMATCH REPAIR PROTEIN MUTS
KeywordsDNA BINDING / MISMATCH RECOGNITION
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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: 2.5 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*GP*TP*GP*GP *CP*AP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,1506
Polymers197,6994
Non-polymers4522
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-83.1 kcal/mol
Surface area69950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.413, 91.810, 260.444
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*GP*TP*GP*GP *CP*AP*GP*CP*T)-3'


Mass: 9304.978 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, 91 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-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


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT CARRIES OUT THE MISMATCH ...FUNCTION: 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. SIMILARITY: 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: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2002 / Details: MIRRORS
RadiationMonochromator: GE220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 68892 / % possible obs: 91.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.08 / % possible all: 60.5
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 15 Å / Num. obs: 75563 / Num. measured all: 382803 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 60.5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.1

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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: 2.5→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.4 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.551 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1330 1.9 %RANDOM
Rwork0.228 ---
obs0.229 66988 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.98 Å20 Å20 Å2
2--8.17 Å20 Å2
3----4.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12171 716 28 89 13004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02113213
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211954
X-RAY DIFFRACTIONr_angle_refined_deg1.4982.04418033
X-RAY DIFFRACTIONr_angle_other_deg0.862327738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90551536
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_restr0.0770.22012
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214152
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022511
X-RAY DIFFRACTIONr_nbd_refined0.2060.22789
X-RAY DIFFRACTIONr_nbd_other0.2210.214011
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.27963
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4811.57676
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.919212329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.37635537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3134.55704
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.41 65
Rwork0.341 3177
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)
13.5957-0.1276-1.19822.15260.1052.87270.0001-0.1578-0.03960.020.0183-0.1470.01660.2134-0.01840.35170.0032-0.00360.2486-0.01090.272238.418910.263233.8466
22.30690.0818-0.10191.8153-0.47232.03490.06780.07640.0634-0.1278-0.0239-0.07770.0128-0.0382-0.0440.22180.01480.00430.0852-0.01650.282712.78729.160718.9134
31.1692-0.1950.84141.2582-0.71272.35150.0586-0.26580.17130.1430.02620.117-0.13520.005-0.08490.29760.01860.03810.18-0.05550.3523-0.916521.496632.8442
41.77080.19323.9963-3.9376-2.97013.7711-0.4305-0.23520.05850.52960.54010.183-0.4637-0.3618-0.10960.38410.03070.10450.2776-0.0580.3417-8.616228.659732.1291
52.58810.18530.59584.1611-0.20510.2205-0.0845-0.17330.0383-0.02920.22870.16960.1311-0.5103-0.14420.40720.0144-0.00710.28040.02310.271742.07416.686576.844
63.5518-0.47852.82441.8297-0.87494.04690.0609-0.5414-0.18950.36040.1065-0.1298-0.0747-0.1427-0.16740.4718-0.01390.05990.4907-0.02350.34228.00249.25954.1046
70.5414-0.0950.820.0166-0.11290.48080.31210.0511-0.21230.1143-0.1438-0.09850.28440.3851-0.16820.5166-0.0619-0.03630.5460.05980.465618.00884.855354.7755
80.18650.1594-0.6961.0448-1.00313.06210.0083-0.11690.0675-0.00890.03940.037-0.08460.0922-0.04770.24340.0078-0.03460.1231-0.0210.3864-6.175734.23755.4172
94.74330.58363.2038-1.40844.399410.9668-0.1995-0.91611.1648-0.2025-0.28290.7289-1.2585-0.41110.48240.4556-0.00630.01480.0807-0.03160.6426-9.668651.33465.8321
103.4939-0.24961.32582.78070.57433.890.09170.06540.18770.13740.18480.43050.209-0.0424-0.27650.34370.06440.03670.0965-0.00120.42830.64359.5793-5.119
114.0763.38322.9063.7022-2.85875.67750.3865-0.7753-0.5550.4222-0.0570.37970.9978-0.9666-0.32950.8303-0.1619-0.03180.61180.02730.66728.200243.629843.5155
122.1345-0.16190.473.2192-0.7363.13220.0250.05610.1066-0.01250.03790.3693-0.2336-0.3016-0.06290.3276-0.01010.01680.188-0.0270.295332.42464.44725.8892
131.74730.03181.17310.8260.03132.15340.06580.0821-0.0447-0.0234-0.06440.01110.11540.131-0.00130.33540.04060.00140.1807-0.04120.307947.000651.306513.5213
141.22691.3284.8995-0.908-0.24396.6542-0.05510.3631-0.0749-0.08390.0583-0.15750.24470.395-0.00320.28570.06960.01580.1414-0.07840.289148.672548.25763.6789
154.52761.07061.73718.2968-1.81781.1254-0.0798-0.0229-0.0501-0.1086-0.159-0.43180.15090.54730.23880.48850.03040.02210.62530.02390.320162.224218.624961.5648
162.8845-1.52641.90912.2281-3.93877.12420.0931-0.0233-0.08870.1478-0.3178-0.1353-0.00680.8960.22470.40850.0129-0.02940.3296-0.08690.410563.920847.937833.4263
170.6898-0.25460.12170.56180.8589-2.8195-0.0236-0.4941-0.08040.3683-0.0395-0.1875-0.21840.11250.0630.4697-0.0604-0.03220.5550.03090.417260.878547.488443.7068
186.232-0.4940.90540.25540.13180.6410.0064-0.1320.184-0.06230.05690.0391-0.0081-0.05-0.06320.2770.008-0.00890.0064-0.03740.289424.000754.3319-6.9092
191.9442-0.03220.333722.27581.6595-0.1892-0.0445-0.0095-0.57590.05830.1674-0.23960.24650.2499-0.12290.3497-0.0062-0.03410.16660.0020.31822.119439.6417-16.4115
203.98381.8071-1.34754.9603-1.11952.7245-0.20960.0526-0.2307-0.37970.33860.38950.1562-0.5191-0.1290.2679-0.0078-0.01950.1284-0.00990.29045.016334.4477-16.2848
211.82162.31312.00741.00870.33656.4176-0.0452-0.016-0.20340.19220.1845-0.56890.05080.6999-0.13920.4656-0.1104-0.01330.5105-0.00640.381549.097814.632951.0477
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 - 18
24X-RAY DIFFRACTION21F14 - 30
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.488

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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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