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- PDB-4b0c: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd... -

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Basic information

Entry
Database: PDB / ID: 4b0c
TitleCrystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with 3-(pentylthio)-4H-1,2,4-triazole
Components3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
KeywordsLYASE / FATTY ACID BIOSYNTHESIS / BACTERIAL VIRULENCE / DRUG DISCOVERY
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
5-(pentylsulfanyl)-1H-1,2,4-triazole / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMoynie, L. / McMahon, S.A. / Duthie, F.G. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Insights Into the Mechanism and Inhibition of the Beta-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase from Pseudomonasaeruginosa.
Authors: Moynie, L. / Leckie, S.M. / Mcmahon, S.A. / Duthie, F.G. / Koehnke, A. / Taylor, J.W. / Alphey, M.S. / Brenk, R. / Smith, A.D. / Naismith, J.H.
History
DepositionJul 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,69910
Polymers93,8435
Non-polymers8565
Water36020
1
A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8804
Polymers37,5372
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-20.6 kcal/mol
Surface area13420 Å2
MethodPISA
2
C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8804
Polymers37,5372
Non-polymers3432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-19.2 kcal/mol
Surface area13420 Å2
MethodPISA
3
E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules

E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8804
Polymers37,5372
Non-polymers3432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3630 Å2
ΔGint-18.8 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.930, 141.700, 78.910
Angle α, β, γ (deg.)90.00, 115.67, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

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
11THRTHRTHRTHRAA2 - 1682 - 168
21THRTHRTHRTHRBB2 - 1682 - 168
12THRTHRPHEPHEAA2 - 1712 - 171
22THRTHRASPASPCC2 - 1692 - 169
13THRTHRTHRTHRAA2 - 1682 - 168
23THRTHRTHRTHRDD2 - 1682 - 168
14LYSLYSTHRTHRAA3 - 1683 - 168
24LYSLYSTHRTHREE3 - 1683 - 168
15THRTHRASPASPBB2 - 1692 - 169
25THRTHRASPASPCC2 - 1692 - 169
16THRTHRPHEPHEBB2 - 1712 - 171
26THRTHRPHEPHEDD2 - 1712 - 171
17LYSLYSSERSERBB3 - 1703 - 170
27LYSLYSSERSEREE3 - 1703 - 170
18THRTHRTHRTHRCC2 - 1682 - 168
28THRTHRTHRTHRDD2 - 1682 - 168
19LYSLYSTHRTHRCC3 - 1683 - 168
29LYSLYSTHRTHREE3 - 1683 - 168
110LYSLYSPHEPHEDD3 - 1713 - 171
210LYSLYSPHEPHEEE3 - 1713 - 171

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(0.3502, -0.6199, 0.7022), (-0.6223, -0.7142, -0.3202), (0.7001, -0.3249, -0.6359)-5.8693, -2.29, 9.5588
2given(0.5053, 0.822, -0.2627), (-0.8234, 0.3682, -0.4317), (-0.2581, 0.4345, 0.8629)3.7286, -0.9416, -4.6357
3given(0.5102, 0.376, 0.7735), (0.3756, -0.9065, 0.1928), (0.7737, 0.1922, -0.6037)-7.6465, -2.8535, 15.6454
4given(-0.496, -0.8284, 0.2602), (-0.8308, 0.3655, -0.4199), (0.2527, -0.4244, -0.8695)-4.2151, -1.1329, 4.2794

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Components

#1: Protein
3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE / BETA-HYDROXYDECANOYL THIOESTER DEHYDRASE


Mass: 18768.533 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: O33877, EC: 4.2.1.60
#2: Chemical
ChemComp-C9H / 5-(pentylsulfanyl)-1H-1,2,4-triazole


Mass: 171.263 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H13N3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.06 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 4.5
Details: PEG MME 5000 13 %, 100 MM SODIUM CITRATE PH 4.5, LITHIUM SULPHATE 0.09 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→35.23 Å / Num. obs: 31096 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.8
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FQ9
Resolution: 2.7→35.23 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 23.919 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.802 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23201 1569 5 %RANDOM
Rwork0.20509 ---
obs0.20643 29525 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20.38 Å2
2---0.38 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 55 20 6569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196700
X-RAY DIFFRACTIONr_bond_other_d0.0060.024618
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9659045
X-RAY DIFFRACTIONr_angle_other_deg1.2253.00111113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6123.243296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.326151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9281548
X-RAY DIFFRACTIONr_chiral_restr0.0790.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217509
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021446
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A59990.06
12B59990.06
21A58980.06
22C58980.06
31A58870.06
32D58870.06
41A60550.05
42E60550.05
51B59590.06
52C59590.06
61B59500.08
62D59500.08
71B60760.04
72E60760.04
81C58960.06
82D58960.06
91C59120.05
92E59120.05
101D60160.07
102E60160.07
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 126 -
Rwork0.324 2108 -
obs--99.55 %
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)
118.5808-2.7698-10.32819.13682.45135.8427-0.4602-0.86990.031-1.15090.749-2.45610.14160.6293-0.28870.21580.01740.19261.1149-0.47141.376538.674-25.0413.958
22.03410.5763-0.6844.7163-0.62264.76830.1237-0.095-0.48350.09980.0305-1.1510.44450.5835-0.15420.06740.0268-0.11120.3987-0.05450.59928.123-24.46314.6
31.48820.63591.6475.5881.06821.8741-0.07170.2667-0.1575-0.19440.2802-1.0653-0.12120.3903-0.20850.0465-0.0566-0.03420.4253-0.09110.37826.875-15.549.043
42.53940.87441.61292.13572.5373.18360.1542-0.044-0.60560.21780.2024-0.23040.25770.2561-0.35660.10530.0632-0.12750.38940.01260.359520.384-25.42114.115
56.09424.4043-2.059811.0936-3.6816.2069-0.35830.32520.2175-0.97540.6748-0.30370.03610.2167-0.31660.1363-0.04690.00870.3598-0.13570.177521.728-15.3797.081
61.2691.0134-1.001711.09551.52228.4917-0.0631-1.03020.00421.92430.2433-1.10450.73240.9677-0.18020.88-0.0254-0.4531.10520.04250.633626.507-11.15838.97
75.7881-0.3234-2.36335.22731.24353.380.0978-0.3314-0.37510.4083-0.0333-0.9362-0.00720.4195-0.06450.1309-0.1007-0.21210.4955-0.03570.467129.278-5.5325.326
82.96322.7999-1.90394.25421.918111.78970.2693-0.2659-0.24990.8663-0.2426-0.27740.6654-0.2192-0.02670.44610.0347-0.07020.4017-0.03130.253417.422-10.75329.248
93.9882-0.6183-1.5415.3725-1.1124.74480.0509-0.2984-0.48860.5206-0.0549-0.52540.31740.05580.0040.2093-0.1225-0.11940.3303-0.09110.280921.392-3.89624.929
108.73455.0607-2.72958.7731-3.14756.2914-0.0271-0.0325-0.24150.30640.248-0.13980.405-0.1364-0.22090.1426-0.0714-0.06210.3457-0.12270.14417.787-8.51324.819
116.334-4.16344.126514.6433-1.23618.12130.20410.10750.5637-1.19510.1086-1.49480.0770.2351-0.31280.4649-0.28540.27550.4219-0.03890.476535.44823.2729.09
121.8671-0.7109-0.22722.59750.92324.1884-0.0418-0.07740.286-0.19880.1242-0.238-0.21740.1237-0.08240.3077-0.23280.06530.3015-0.12230.369925.93420.07720.159
133.8604-1.1452-2.04755.26410.05343.58870.08860.17880.16-0.6026-0.12540.1506-0.5702-0.22520.03680.3344-0.1286-0.03290.2717-0.08420.314721.61116.4214.443
144.7152-4.93087.57758.2309-2.573129.22190.13390.21150.2266-0.7839-0.37190.50570.48030.54710.2380.5201-0.1301-0.20720.4427-0.18990.620120.45812.4215.263
158.14320.14860.99466.678-12.450634.2198-0.20770.55950.4161-0.77740.28850.6242-0.7979-1.5837-0.08080.75140.0106-0.10470.3202-0.19190.429316.65218.23510.528
166.1469-3.74990.07117.88433.49794.2524-0.3294-0.69360.4351-0.51060.04930.6098-0.0856-0.20010.28010.3611-0.0646-0.11880.4391-0.16140.49056.6133.78735.188
1710.5689-1.827-2.43370.81051.89568.080.1965-0.2403-0.3858-0.5721-0.17320.0127-0.9433-0.317-0.02330.90740.102-0.05430.3397-0.03510.570310.85433.12719.439
184.5357-2.2049-2.01287.49483.57874.5265-0.3606-0.59130.0923-0.0641-0.04180.46510.3951-0.29050.40240.2196-0.0421-0.06830.38-0.10590.46147.77523.68130.644
193.8022-1.3026-1.91164.26051.93044.67280.1578-0.08620.0412-1.1313-0.40491.0787-0.4836-0.74380.24710.54910.0294-0.330.4318-0.13880.63484.58127.37619.062
203.955-3.01521.62699.3996-3.594114.80250.0674-0.11740.0453-0.0985-0.44880.95430.6764-0.11440.38130.1687-0.0927-0.05140.422-0.13260.6015.94321.18925.707
2114.9464-3.41533.97954.0156-1.12479.4111-0.6486-1.1421-1.12570.35030.10490.43141.5318-0.16410.54370.88770.13610.32880.4090.310.5504-1.45-44.5321.228
222.8659-0.774-1.31591.79160.79663.2426-0.3281-0.2542-0.48220.07530.0212-0.04410.64250.45140.30690.3470.09790.08090.18160.15910.23535.934-39.7059.202
233.613-0.64-1.63941.6879-1.46354.8328-0.2569-0.1637-0.45960.1176-0.0652-0.00490.17560.10260.32220.19020.009-0.02710.18170.02620.1477-2.23-32.9559.97
244.11841.2914-0.51840.5715-1.0795.1108-0.1739-0.332-0.447-0.1426-0.1652-0.19330.48870.35710.33910.19220.0969-0.00490.17970.12520.181610.461-33.4638.071
255.56971.2268-3.0654.9169-0.55074.7351-0.0179-0.09290.57790.1521-0.00530.4690.1047-0.1680.02330.2110.0114-0.03890.2073-0.00470.1438-2.709-28.70610.189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 77
3X-RAY DIFFRACTION3A78 - 113
4X-RAY DIFFRACTION4A114 - 132
5X-RAY DIFFRACTION5A133 - 166
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 86
8X-RAY DIFFRACTION8B87 - 113
9X-RAY DIFFRACTION9B114 - 138
10X-RAY DIFFRACTION10B139 - 171
11X-RAY DIFFRACTION11C2 - 22
12X-RAY DIFFRACTION12C23 - 86
13X-RAY DIFFRACTION13C87 - 134
14X-RAY DIFFRACTION14C135 - 152
15X-RAY DIFFRACTION15C153 - 169
16X-RAY DIFFRACTION16D2 - 45
17X-RAY DIFFRACTION17D46 - 77
18X-RAY DIFFRACTION18D78 - 109
19X-RAY DIFFRACTION19D110 - 135
20X-RAY DIFFRACTION20D138 - 171
21X-RAY DIFFRACTION21E2 - 23
22X-RAY DIFFRACTION22E24 - 77
23X-RAY DIFFRACTION23E78 - 113
24X-RAY DIFFRACTION24E114 - 132
25X-RAY DIFFRACTION25E133 - 171

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