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- PDB-5l6h: Uba1 in complex with Ub-ABPA3 covalent adduct -

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Basic information

Entry
Database: PDB / ID: 5l6h
TitleUba1 in complex with Ub-ABPA3 covalent adduct
Components
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-activating enzyme E1 1
KeywordsLIGASE / E1 enzyme / ubiquitin activation / Uba1 inhibitor / adenosyl sulfamate
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / Neddylation / ubiquitin activating enzyme activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation ...E1 ubiquitin-activating enzyme / Neddylation / ubiquitin activating enzyme activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation / ubiquitin-dependent protein catabolic process / protein ubiquitination / structural constituent of ribosome / DNA damage response / ubiquitin protein ligase binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain ...Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / Ubiquitin conserved site / Ubiquitin domain / 3-Layer(bba) Sandwich / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6O2 / ACETATE ION / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-activating enzyme E1 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMisra, M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFZ82; HS Germany
CitationJournal: Structure / Year: 2017
Title: Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme.
Authors: Misra, M. / Kuhn, M. / Lobel, M. / An, H. / Statsyuk, A.V. / Sotriffer, C. / Schindelin, H.
History
DepositionMay 30, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionJun 14, 2017ID: 3CMM, 4NNJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 7, 2024Group: 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_ncs_dom_lim
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-40S ribosomal protein S31
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-40S ribosomal protein S31
E: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,99130
Polymers254,5265
Non-polymers2,46525
Water17,853991
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,30815
Polymers122,9792
Non-polymers1,32913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-40S ribosomal protein S31
E: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,68315
Polymers131,5473
Non-polymers1,13612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.048, 194.098, 230.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13B
23E
14D
24E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAHISHISAA11 - 102311 - 1023
21ALAALAHISHISCC11 - 102311 - 1023
12METMETGLYGLYBB1 - 761 - 76
22METMETGLYGLYDD1 - 761 - 76
13METMETLEULEUBB1 - 711 - 71
23METMETLEULEUEE1 - 711 - 71
14METMETLEULEUDD1 - 711 - 71
24METMETLEULEUEE1 - 711 - 71

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 5 molecules ACBDE

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 114409.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UBA1, YKL210W / Production host: Escherichia coli (E. coli) / References: UniProt: P22515, E1 ubiquitin-activating enzyme
#2: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8568.769 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P05759

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Non-polymers , 7 types, 1016 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-6O2 / [(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate / ABPA3


Mass: 446.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N6O6S
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 143279 / % possible obs: 99.5 % / Redundancy: 7.5 % / Rsym value: 0.107 / Net I/σ(I): 13.3
Reflection shellHighest resolution: 2.3 Å / Rsym value: 1.866

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NNJ

4nnj


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 14.453 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21837 7006 4.9 %RANDOM
Rwork0.1725 ---
obs0.17475 135949 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.32 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17654 0 151 991 18796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01918369
X-RAY DIFFRACTIONr_bond_other_d0.0090.0217550
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.97824881
X-RAY DIFFRACTIONr_angle_other_deg1.533340619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8152296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81625.388876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.331153290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8281584
X-RAY DIFFRACTIONr_chiral_restr0.1280.22795
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02120786
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024036
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7222.6219016
X-RAY DIFFRACTIONr_mcbond_other1.7152.6219014
X-RAY DIFFRACTIONr_mcangle_it2.6953.92611276
X-RAY DIFFRACTIONr_mcangle_other2.6953.92611277
X-RAY DIFFRACTIONr_scbond_it2.5052.9079353
X-RAY DIFFRACTIONr_scbond_other2.5042.9089354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9644.2413576
X-RAY DIFFRACTIONr_long_range_B_refined6.96821.33120760
X-RAY DIFFRACTIONr_long_range_B_other6.95720.89520431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1276040.07
12C1276040.07
21B95180.09
22D95180.09
31B87300.13
32E87300.13
41D85540.14
42E85540.14
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 525 -
Rwork0.309 9850 -
obs--99.97 %
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)
11.64620.37070.02681.297-0.03470.6037-0.01240.0060.0436-0.1307-0.0340.44110.0425-0.15750.04640.26120.019-0.05810.2581-0.00130.1653-20.598927.9951-42.3596
25.06422.39831.46035.22651.07752.6068-0.07140.13730.0705-0.11860.0177-0.3006-0.1490.32390.05370.18260.01530.02540.2530.06220.06613.209857.0429-42.0816
30.618-0.20830.09591.37550.47770.9350.0029-0.0459-0.18220.05640.02790.0510.12970.0155-0.03090.18560.01520.00010.23210.04150.0572-8.031718.2852-31.6048
41.76670.5543-1.46013.7606-1.42134.1003-0.0737-0.62980.14230.4398-0.0854-0.3877-0.27970.45440.15920.37560.0544-0.02860.3959-0.0450.0829-10.529961.9742-4.9713
50.3399-0.40880.1470.98440.29560.6581-0.0173-0.0527-0.07360.12030.01110.10210.0215-0.0490.00620.2180.01820.02870.24050.03380.0274-5.265432.9453-22.3732
62.89490.63261.53371.83680.07044.94040.0429-0.30280.30520.2790.10750.1482-0.3273-0.437-0.15040.42540.1196-0.02430.28040.01830.134317.90615.24143.0067
75.18370.52890.52126.81950.36772.4060.00920.24090.1107-0.3010.0423-0.8025-0.00170.3101-0.05160.20540.03710.01710.28440.04220.214915.289931.6651-37.5667
85.83252.1634-1.84581.2998-1.62632.3945-0.0212-0.12570.2234-0.0432-0.1173-0.04930.08560.21170.13850.24730.0796-0.01660.1849-0.0180.11043.378230.8378-31.1192
92.40510.1429-0.12751.08730.14181.8602-0.092-0.2471-0.04990.23510.07760.27780.1147-0.06250.01440.2010.04150.04720.22520.06350.0828-35.995764.5221-39.8007
103.57-1.6516-1.98784.40191.50314.06260.06120.2348-0.1166-0.52980.0326-0.57030.21540.5344-0.09380.28530.03040.04890.37550.01780.1643-2.925552.1313-60.2511
111.3232-0.50180.39181.6449-0.09051.5306-0.059-0.01790.17820.06070.05320.0599-0.2938-0.00740.00580.19880.02120.02930.21040.05570.0536-36.031179.3003-51.1092
120.1193-0.27850.15612.7309-0.08850.26690.13560.17520.0414-0.8494-0.1321-0.41320.10710.209-0.00350.43950.06090.09040.44660.07040.0819-28.312264.374-75.0021
133.9298-1.13121.67142.6067-0.02772.53330.16540.7763-0.1025-0.644-0.0791-0.09530.39940.2121-0.08630.59070.0679-0.09340.4223-0.05070.0891-29.046534.2307-83.0707
140.36340.10010.13220.2271-0.02881.47470.01490.11850.0074-0.0065-0.0198-0.0346-0.15730.13280.00490.16690.00060.00570.26410.05010.0191-27.698972.8947-65.2646
153.620.6875-0.53361.9897-0.25684.98420.06650.1521-0.2506-0.1330.0150.21610.2621-0.4266-0.08150.30070.0270.00430.27020.06860.0959-38.296388.0888-98.2918
164.4351-2.614-0.8616.7598-1.17814.34860.10570.00050.5551-0.277-0.0264-0.8948-0.35630.4073-0.07940.2603-0.04820.08810.3850.06930.2874-8.841577.7541-66.8707
1712.26612.98043.13431.2369-0.03532.07320.0366-0.091-0.592-0.1167-0.0477-0.28750.13040.02530.01110.31320.02040.08760.23720.00740.2312-20.687971.209-65.4698
180.3716-1.25240.12737.1526-1.18210.2429-0.19740.302-0.3073-0.55320.14640.18750.2026-0.26830.0511.4289-0.07430.13871.5565-0.17621.4378.846459.4716-81.7522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 197
2X-RAY DIFFRACTION2A198 - 264
3X-RAY DIFFRACTION3A265 - 624
4X-RAY DIFFRACTION4A625 - 810
5X-RAY DIFFRACTION5A811 - 925
6X-RAY DIFFRACTION6A926 - 1024
7X-RAY DIFFRACTION7B1 - 65
8X-RAY DIFFRACTION8B66 - 76
9X-RAY DIFFRACTION9C11 - 166
10X-RAY DIFFRACTION10C167 - 264
11X-RAY DIFFRACTION11C265 - 545
12X-RAY DIFFRACTION12C546 - 624
13X-RAY DIFFRACTION13C625 - 844
14X-RAY DIFFRACTION14C845 - 925
15X-RAY DIFFRACTION15C926 - 1024
16X-RAY DIFFRACTION16D1 - 65
17X-RAY DIFFRACTION17D66 - 76
18X-RAY DIFFRACTION18E1 - 72

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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

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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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