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- PDB-4xrp: Structure of the Pnkp1/Rnl/Hen1 RNA repair complex -

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Basic information

Entry
Database: PDB / ID: 4xrp
TitleStructure of the Pnkp1/Rnl/Hen1 RNA repair complex
Components
  • Hen1
  • Pnkp1
  • Rnl
KeywordsPROTEIN BINDING / RNA repair / kinase / phosphatase / methyltransferase / ligase
Function / homology
Function and homology information


deoxynucleotide 3'-phosphatase activity / RNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / ATP binding / metal ion binding
Similarity search - Function
Polynucleotide kinase PNKP, C-terminal phosphatase domain / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / AAA domain / HAD superfamily / HAD-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein / Polynucleotide kinase / Polynucleotide kinase-phosphatase ligase domain-containing protein
Similarity search - Component
Biological speciesCapnocytophaga gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsHuang, R.H. / Wang, P.
CitationJournal: Nat Commun / Year: 2015
Title: Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.
Authors: Wang, P. / Selvadurai, K. / Huang, R.H.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pnkp1
B: Rnl
C: Hen1
D: Pnkp1
E: Rnl
F: Hen1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,39725
Polymers268,8816
Non-polymers1,51619
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22400 Å2
ΔGint-226 kcal/mol
Surface area100540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.160, 179.201, 114.333
Angle α, β, γ (deg.)90.000, 103.700, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPHEPHEchain AAA2 - 3122 - 312
21SERSERPHEPHEchain DDD2 - 3122 - 312
12METMETLEULEUchain BBB1 - 3941 - 394
22GLUGLULEULEUchain EEE2 - 3942 - 394
13METMETARGARGchain CCC1 - 4351 - 435
23METMETARGARGchain FFF1 - 4351 - 435

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Pnkp1


Mass: 36317.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Strain: ATCC 33624 / Gene: CAPGI0001_2485 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M8N3
#2: Protein Rnl


Mass: 46561.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Strain: ATCC 33624 / Gene: CAPGI0001_2487 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M8N4
#3: Protein Hen1


Mass: 51561.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Strain: ATCC 33624 / Gene: CAPGI0001_1566 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M7I7

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Non-polymers , 5 types, 112 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.11 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2014 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 65439 / % possible obs: 98.4 % / Redundancy: 7.5 % / Net I/σ(I): 17.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX(phenix.refine: dev_1624)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→47.206 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1990 3.04 %
Rwork0.1748 --
obs0.1767 65439 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.84 Å2 / Biso mean: 70.6692 Å2 / Biso min: 30.42 Å2
Refinement stepCycle: final / Resolution: 3.3→47.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18711 0 84 93 18888
Biso mean--96.95 47.67 -
Num. residues----2255
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2864X-RAY DIFFRACTION8.643TORSIONAL
12D2864X-RAY DIFFRACTION8.643TORSIONAL
21B3650X-RAY DIFFRACTION8.643TORSIONAL
22E3650X-RAY DIFFRACTION8.643TORSIONAL
31C3878X-RAY DIFFRACTION8.643TORSIONAL
32F3878X-RAY DIFFRACTION8.643TORSIONAL
Refinement TLS params.Method: refined / Origin x: 97.2875 Å / Origin y: 5.5196 Å / Origin z: 142.3371 Å
111213212223313233
T0.4694 Å2-0.0628 Å2-0.0428 Å2-0.2737 Å20.0404 Å2--0.4333 Å2
L0.9007 °2-0.2234 °2-0.0187 °2-0.2059 °2-0.029 °2--0.0616 °2
S0.1172 Å °-0.0152 Å °-0.136 Å °-0.0318 Å °-0.099 Å °0.0076 Å °-0.0033 Å °0.0113 Å °-0.0209 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )A2 - 312
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )A401 - 404
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )A501 - 507
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )C1 - 435
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )C501 - 504
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )C601 - 622
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )B1 - 394
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )B401 - 404
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )B501 - 518
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )E2 - 394
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )E401 - 402
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )E501 - 517
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )D2 - 312
14X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )D401 - 402
15X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )D501 - 509
16X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )F1 - 435
17X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )F501 - 503
18X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )F601 - 620

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