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- PDB-1tez: COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS -

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Basic information

Entry
Database: PDB / ID: 1tez
TitleCOMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS
Components
  • 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'
  • 5'-D(*TP*CP*GP*C)-3'
  • 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'
  • 5'-D(P*GP*CP*CP*GP*A)-3'
  • Deoxyribodipyrimidine photo-lyase type I
KeywordsLYASE/DNA / PHOTOLYASE / DNA REPAIR / LIGHT-DRIVEN ELECTRON TRANSFER / LYASE-DNA COMPLEX
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleobase-containing compound metabolic process / response to stress / response to light stimulus / FAD binding / DNA repair / DNA binding
Similarity search - Function
DNA photolyase class 1, 8-HDF type / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase ...DNA photolyase class 1, 8-HDF type / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-HDF / DNA / DNA (> 10) / Deoxyribodipyrimidine photo-lyase / Deoxyribodipyrimidine photo-lyase type I
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 6301 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEssen, L.-O. / Carell, T. / Mees, A. / Klar, T.
Citation
Journal: Science / Year: 2004
Title: Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair
Authors: Mees, A. / Klar, T. / Gnau, P. / Hennecke, U. / Eker, A.P.M. / Carell, T. / Essen, L.-O.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal Structure of DNA Photolyase from Anacystis
Authors: Tamada, T. / Kitadokoro, K. / Higuchi, Y. / Inaka, K. / Yasui, A. / De Ruiter, P.E. / Eker, A.P. / Miki, K.
History
DepositionMay 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 30, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / ndb_struct_na_base_pair_step ...database_PDB_caveat / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms
Item: _ndb_struct_na_base_pair_step.inclination / _pdbx_struct_assembly.oligomeric_count ..._ndb_struct_na_base_pair_step.inclination / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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.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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jul 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'
J: 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'
K: 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'
L: 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'
M: 5'-D(*TP*CP*GP*C)-3'
N: 5'-D(P*GP*CP*CP*GP*A)-3'
O: 5'-D(*TP*CP*GP*C)-3'
P: 5'-D(P*GP*CP*CP*GP*A)-3'
A: Deoxyribodipyrimidine photo-lyase type I
B: Deoxyribodipyrimidine photo-lyase type I
C: Deoxyribodipyrimidine photo-lyase type I
D: Deoxyribodipyrimidine photo-lyase type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,90422
Polymers231,25912
Non-polymers4,64410
Water29,0761614
1
I: 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'
J: 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'
A: Deoxyribodipyrimidine photo-lyase type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6576
Polymers59,4833
Non-polymers1,1733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'
L: 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'
B: Deoxyribodipyrimidine photo-lyase type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6576
Polymers59,4833
Non-polymers1,1733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: 5'-D(*TP*CP*GP*C)-3'
N: 5'-D(P*GP*CP*CP*GP*A)-3'
C: Deoxyribodipyrimidine photo-lyase type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2955
Polymers56,1463
Non-polymers1,1492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: 5'-D(*TP*CP*GP*C)-3'
P: 5'-D(P*GP*CP*CP*GP*A)-3'
D: Deoxyribodipyrimidine photo-lyase type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2955
Polymers56,1463
Non-polymers1,1492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.815, 88.505, 161.622
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9812, -0.1669, -0.0968), (-0.173, 0.9832, 0.0584), (0.0854, 0.0741, -0.9936)168.70441, 12.1157, 69.5988
2given(-0.9802, 0.174, -0.0945), (0.1673, 0.9831, 0.0748), (0.1059, 0.0575, -0.9927)168.664, -2.3893, 83.7414
3given(-0.9802, -0.1704, -0.1005), (0.1768, -0.9826, -0.0577), (-0.0889, -0.0744, 0.9933)81.9103, -0.9482, 11.4041
4given(1, 0.0032, -0.0054), (0.0032, -1, 0.0008), (-0.0053, -0.0008, -1)87.1324, 11.2315, 81.0413

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Components

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DNA chain , 4 types, 8 molecules IKJLMONP

#1: DNA chain 5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'


Mass: 3259.219 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Formacetal linkage replaces phosphate linkage between T7 and T8 of chains I and K
Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'


Mass: 2749.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*TP*CP*GP*C)-3'


Mass: 1166.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain 5'-D(P*GP*CP*CP*GP*A)-3'


Mass: 1505.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 4 molecules ABCD

#5: Protein
Deoxyribodipyrimidine photo-lyase type I / E.C.4.1.99.3


Mass: 53474.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SYNTHETIC DNA OLIGONUCLEOTIDES ENGINEERED AS COUNTERSTRAND
Source: (gene. exp.) Synechococcus elongatus PCC 6301 (bacteria)
Species: Synechococcus elongatus / Strain: PCC 6301 / Cellular location: CYTOPLASM / Gene: Synpcc7942_0112 / Plasmid: PET3A / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: Q31S25, UniProt: P05327*PLUS, deoxyribodipyrimidine photo-lyase

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Non-polymers , 4 types, 1624 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical
ChemComp-HDF / 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE


Mass: 363.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17N3O7
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1614 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCOMPOUND THE CYCLOBUTANE RING OF THE CPD-DAMAGE I7-I8 AND K7-K8 WAS FOUND TO BE CLEAVED
Nonpolymer detailsHETEROGEN DESOXYTHYMIDINE NUCLEOSIDE WITH FORMACETAL LINKAGE AT 5'-HYDROXYL

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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: 2.44 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2MgCl211
3Tris-HCl11
4PEG 400012
5MgCl212
6Tris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9796 / Wavelength: 0.9796 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 27, 2004 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 218105 / Num. obs: 218105 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.1 / % possible all: 81.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNF

1qnf


Resolution: 1.8→29.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2423887.54 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 7425 3.4 %SHELLS
Rwork0.205 ---
obs0.2051 218104 96.1 %-
all-218104 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.7551 Å2 / ksol: 0.37764 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.7 Å20 Å2-0.35 Å2
2---0.46 Å20 Å2
3----5.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15106 1012 474 1614 18206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 1188 3.8 %
Rwork0.285 29841 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMDNA-RNA_NEW.TOP
X-RAY DIFFRACTION4COFACS.PARAMCOFACS.TOP

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