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- PDB-5v10: Crystal structure of the putative tol-pal system-associated acyl-... -

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Basic information

Entry
Database: PDB / ID: 5v10
TitleCrystal structure of the putative tol-pal system-associated acyl-CoA thioesterase from Pseudomonas aeruginosa PAO1
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / order-disorder / Center for Structural Genomics of Infectious Diseases (CSGID)
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
Tol-Pal system-associated acyl-CoA thioesterase / Acyl-CoA thioester hydrolase YbgC/YbaW family / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
4HBT domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBorek, D. / Wawrzak, Z. / Grimshaw, S. / Sandoval, J. / Evdokimova, E. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of the putative tol-pal system-associated acyl-CoA thioesterase from Pseudomonas aeruginosa PAO1
Authors: Borek, D. / Wawrzak, Z. / Grimshaw, S. / Sandoval, J. / Evdokimova, E. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0435
Polymers33,9362
Non-polymers1063
Water1,40578
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,08510
Polymers67,8734
Non-polymers2136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8230 Å2
ΔGint-102 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.994, 62.279, 52.792
Angle α, β, γ (deg.)90.00, 112.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 9 - 137 / Label seq-ID: 12 - 140

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Uncharacterized protein


Mass: 16968.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0968 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q9I4Z5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Succinic Acid pH 7.0, 15 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→51.31 Å / Num. obs: 21234 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.049 / Net I/σ(I): 13.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 659 / CC1/2: 0.82 / Rpim(I) all: 0.305 / % possible all: 57.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S5U
Resolution: 1.9→51.31 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.692 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.21
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AUTHORS STATE THAT THE R-FREE FACTOR VALUES ARE HIGHER DUE TO ORDER-DISORDER PRESENT IN THE CRYSTAL LATTICE. THEY DECIDED NOT TO MODEL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AUTHORS STATE THAT THE R-FREE FACTOR VALUES ARE HIGHER DUE TO ORDER-DISORDER PRESENT IN THE CRYSTAL LATTICE. THEY DECIDED NOT TO MODEL IT. HOWEVER, THE DIFFRACTION IMAGES FOR THIS PROJECT ARE AVAILABLE AT THE HTTPS://WWW.PROTEINDIFFRACTION.ORG/PROJECT/5V10/ SO THAT OTHER RESEARCHERS CAN MODEL NON-BRAGG DIFFRACTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.28308 952 5.1 %RANDOM
Rwork0.21991 ---
obs0.22315 17785 80.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.1 Å2
2---0.35 Å20 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.9→51.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 3 78 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192227
X-RAY DIFFRACTIONr_bond_other_d0.0020.022112
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9613004
X-RAY DIFFRACTIONr_angle_other_deg1.02134839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87621.949118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00615380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2951531
X-RAY DIFFRACTIONr_chiral_restr0.1050.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02525
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_it8.7081.8291086
X-RAY DIFFRACTIONr_mcbond_other8.7061.8261085
X-RAY DIFFRACTIONr_mcangle_it11.4622.6921357
X-RAY DIFFRACTIONr_mcangle_other11.4582.6951358
X-RAY DIFFRACTIONr_scbond_it11.5852.5051140
X-RAY DIFFRACTIONr_scbond_other11.5832.5081141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.7313.4351648
X-RAY DIFFRACTIONr_long_range_B_refined17.7422.8272372
X-RAY DIFFRACTIONr_long_range_B_other17.74422.8112366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7746 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 21 -
Rwork0.211 439 -
obs--26.92 %
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)
19.68660.70970.40191.9563-2.74434.0602-0.2366-0.14040.3819-0.0950.1076-0.05380.0942-0.16070.1290.049-0.04350.01490.0968-0.04080.031-21.4811-7.6328-5.7736
21.0440.28882.74864.79660.61887.2414-0.0609-0.0680.008-0.29290.05370.3525-0.1504-0.17430.00730.0480.0011-0.02020.09620.01460.0659-28.3906-1.90315.6278
30.21030.13751.29910.17211.03448.4438-0.0265-0.0424-0.03960.03380.1020.0444-0.080.0137-0.07550.11730.08020.06960.20560.09490.1003-24.56584.209516.9924
40.5348-0.96120.47811.7279-0.85950.4362-0.1246-0.05430.0190.23290.0999-0.0379-0.1554-0.06650.02470.24180.0625-0.0080.10240.01120.0358-15.11247.164723.9696
50.73030.27891.49151.85021.05733.2078-0.0675-0.0107-0.0026-0.04530.0591-0.0586-0.2068-0.00240.00850.1519-0.0215-0.01110.0597-0.00560.0618-10.67914.515516.447
61.9921.6510.39911.78030.4950.15010.0750.1315-0.0943-0.0031-0.0462-0.11620.0053-0.0503-0.02870.0717-0.01790.00880.1182-0.02410.067-21.7377-8.03111.1161
78.7865-2.59690.60884.6481-3.29952.5604-0.29850.2765-0.18850.09420.32240.0197-0.0031-0.331-0.02390.1029-0.0512-0.05270.09590.02740.1085-23.828-18.969612.8934
810.3983-1.4602-5.65985.7297-1.08293.7201-0.46920.0848-0.25620.05150.37140.1140.2541-0.17420.09780.1231-0.0239-0.00150.0398-0.02220.1041-18.1666-23.155412.2006
99.18567.6348-1.42087.1985-0.60780.6064-0.04630.128-0.03640.10560.0967-0.0970.1019-0.0228-0.05040.0469-0.0072-0.01170.0567-0.01960.0701-9.4299-12.53458.19
103.8917-5.1525-0.5618.3155-0.09440.56350.2410.09530.1302-0.2789-0.1038-0.005-0.0947-0.0084-0.13720.1263-0.04970.0460.06870.0060.0978-9.8625.56035.5875
112.3460.47120.94220.8429-0.35820.7824-0.3410.11310.07210.20410.2511-0.0424-0.3578-0.10840.090.24350.0645-0.02650.08480.01730.0598-20.48049.881716.1712
121.0747-1.925-3.16525.88415.80069.332-0.0387-0.00980.006-0.02870.04440.10420.09490.0337-0.00570.0532-0.0093-0.01890.08-0.00660.0463-19.6219-4.51832.594
134.8987-3.47042.12159.5598-0.34551.11750.16910.5214-0.1308-0.039-0.12060.01250.07530.255-0.04850.06070.0145-0.00590.0852-0.05050.0608-13.6761-17.3392-2.5808
141.7061-2.6665-0.34925.0718-0.02680.45220.07850.1790.006-0.2428-0.02740.03010.0283-0.1971-0.05110.0729-0.01880.01970.0989-0.00810.0744-15.48-5.20362.6653
156.161-3.192-0.70441.67630.36050.0817-0.1293-0.0620.24250.0810.1366-0.11320.0194-0.0094-0.00730.08460.02320.01610.3260.05050.0752-23.138110.57038.8091
161.8392-2.42650.31714.07640.00290.8532-0.06140.11510.0668-0.04340.1897-0.2132-0.09360.0035-0.12840.0522-0.03690.02440.1986-0.0120.0577-14.35070.95254.7884
171.1359-2.27510.8436.3457-0.38281.5832-0.05670.00770.03170.2001-0.04280.0003-0.0151-0.02460.09950.10890.0107-0.07840.012-0.03460.1361-11.8671-23.74849.6092
180.5612-1.0186-0.89763.8774-1.10835.177-0.0786-0.07460.0878-0.05330.0852-0.29610.39440.209-0.00660.05710.0155-0.02870.0221-0.02940.1035-9.1088-25.33538.8826
199.1754-1.58311.09451.10361.35943.0170.4343-0.223-0.0303-0.0955-0.0722-0.18550.0152-0.2285-0.36210.1133-0.0131-0.02850.1092-0.02870.0904-21.4872-20.31120.6645
207.45027.147-0.02648.3911-4.232511.5321-0.22130.3518-0.0269-0.04380.44910.0581-0.4557-0.3079-0.22790.0488-0.00910.03420.0868-0.08960.1512-28.4852-15.8894-0.1022
210.57032.2768-0.89899.64-3.78251.56360.0545-0.1067-0.07220.0837-0.2154-0.2602-0.00830.23220.16090.0404-0.00230.01330.33570.10640.058111.4128-2.380219.6983
220.30860.5846-0.13421.2101-0.59581.25750.1687-0.08860.00150.2651-0.1003-0.0030.3708-0.2954-0.06840.3523-0.1352-0.02660.18650.00250.0454-0.52-9.505428.322
232.88770.57293.38373.19740.64713.96590.1939-0.1764-0.0975-0.2708-0.07080.12950.2325-0.1992-0.12320.1289-0.0233-0.0020.0772-0.03220.0446-6.767-14.116521.831
241.217-0.9121-1.21890.86050.1854.35880.04760.00510.0614-0.0510.0189-0.03050.174-0.0444-0.06650.1360.01190.03920.0545-0.0070.0688-5.6581-7.798317.1979
250.7941-0.50610.18811.25380.48950.44680.06850.1007-0.0925-0.0509-0.04630.06760.00010.0568-0.02230.0621-0.0570.01730.1289-0.00970.0587-0.1576-0.581218.6456
262.91981.08564.93680.40531.83668.3511-0.10610.28820.0171-0.03690.08910.0098-0.190.47890.0170.117-0.02630.04380.1551-0.01070.04677.51226.50817.3113
272.7994-1.5004-1.331511.7358-0.74940.8426-0.8736-1.01560.3543-0.38030.9825-0.37430.47650.4759-0.10890.56280.0681-0.23150.5931-0.00470.13519.751212.509521.3316
2810.5849-5.09335.09713.93390.51688.4087-0.4008-0.02750.48410.14320.0955-0.1904-0.3210.1770.30530.1431-0.1019-0.01880.0873-0.01630.10914.402520.077420.4673
295.16822.54525.36371.86511.78076.9354-0.53040.35080.5621-0.1820.16060.4629-0.48950.35450.36980.2427-0.03950.03220.07780.05850.1524-1.407313.45112.9729
301.6068-2.96060.7665.4609-1.32282.93650.06520.1112-0.0644-0.1013-0.18620.12970.21370.20680.12090.03750.02420.00720.111-0.02840.0779-1.2014-7.48588.5165
310.50470.99410.15362.92450.56770.1730.01780.0943-0.09530.04990.0133-0.13440.0810.0835-0.03110.14490.1062-0.03080.2623-0.04340.03175.0146-10.164421.5628
320.1235-0.9953-0.083213.6721-1.73471.22910.0802-0.0114-0.0246-0.1633-0.2636-0.0765-0.21730.26250.18340.1102-0.0187-0.01550.11670.0330.05518.016610.79084.8457
332.0743-2.33990.88646.5039-4.77544.070.19930.08180.07570.0639-0.2605-0.1096-0.19390.21860.06120.0502-0.00840.02930.1281-0.00670.05785.18016.32647.0167
342.13750.3582-1.4482.9962-5.13289.12640.09250.0226-0.0757-0.1737-0.2385-0.07060.25410.40310.1460.05110.02640.00440.1151-0.04340.05077.7843-10.298515.3129
354.1104-1.48384.78339.1847-5.49047.20440.18530.2492-0.199-0.2502-0.0069-0.03910.29430.2537-0.17840.06560.05450.01440.0798-0.01210.03018.1452-13.950514.7151
360.7368-1.51070.37638.8875-1.04920.27610.06320.1930.0683-0.301-0.0474-0.21360.05230.1356-0.01570.04640.00850.00510.1182-0.02150.06132.0177-1.85817.5995
370.4132-1.27861.00673.9584-3.11722.455-0.1945-0.04810.01090.60510.1605-0.0396-0.473-0.12810.03390.1584-0.03320.02230.08810.02160.0825-0.750615.72469.8197
380.0626-0.45330.04453.5355-0.30840.0336-0.0334-0.0176-0.03750.16460.06690.0964-0.0398-0.0197-0.03350.15870.05630.04890.05450.04340.1474-5.597722.763112.8148
391.7171-0.705-1.96820.28960.80842.25740.1767-0.11460.183-0.07090.0447-0.0792-0.19510.1208-0.22140.0649-0.0781-0.04330.10170.07480.18416.456620.84249.9893
404.01584.80391.08657.83474.40454.91210.40410.0534-0.00660.2116-0.3673-0.0289-0.2977-0.6164-0.03680.12-0.0066-0.04870.21910.05480.092513.008515.477710.3563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 7
2X-RAY DIFFRACTION2A8 - 12
3X-RAY DIFFRACTION3A13 - 16
4X-RAY DIFFRACTION4A17 - 23
5X-RAY DIFFRACTION5A24 - 34
6X-RAY DIFFRACTION6A35 - 48
7X-RAY DIFFRACTION7A49 - 54
8X-RAY DIFFRACTION8A55 - 60
9X-RAY DIFFRACTION9A61 - 66
10X-RAY DIFFRACTION10A67 - 72
11X-RAY DIFFRACTION11A73 - 81
12X-RAY DIFFRACTION12A82 - 87
13X-RAY DIFFRACTION13A88 - 92
14X-RAY DIFFRACTION14A93 - 100
15X-RAY DIFFRACTION15A101 - 105
16X-RAY DIFFRACTION16A106 - 116
17X-RAY DIFFRACTION17A117 - 122
18X-RAY DIFFRACTION18A123 - 127
19X-RAY DIFFRACTION19A128 - 136
20X-RAY DIFFRACTION20A137 - 142
21X-RAY DIFFRACTION21B9 - 14
22X-RAY DIFFRACTION22B15 - 19
23X-RAY DIFFRACTION23B20 - 26
24X-RAY DIFFRACTION24B27 - 32
25X-RAY DIFFRACTION25B33 - 39
26X-RAY DIFFRACTION26B40 - 44
27X-RAY DIFFRACTION27B45 - 52
28X-RAY DIFFRACTION28B53 - 58
29X-RAY DIFFRACTION29B59 - 64
30X-RAY DIFFRACTION30B65 - 73
31X-RAY DIFFRACTION31B74 - 84
32X-RAY DIFFRACTION32B85 - 91
33X-RAY DIFFRACTION33B92 - 98
34X-RAY DIFFRACTION34B99 - 103
35X-RAY DIFFRACTION35B104 - 109
36X-RAY DIFFRACTION36B110 - 114
37X-RAY DIFFRACTION37B115 - 120
38X-RAY DIFFRACTION38B121 - 126
39X-RAY DIFFRACTION39B127 - 131
40X-RAY DIFFRACTION40B132 - 138

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