[English] 日本語
Yorodumi
- PDB-5ugs: Crystal structure of M. tuberculosis InhA inhibited by PT501 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ugs
TitleCrystal structure of M. tuberculosis InhA inhibited by PT501
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / bacterial enoyl-ACP reductase / diphenylether / residence time
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-XT5 / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEltschkner, S. / Pschibul, A. / Spagnuolo, L.A. / Yu, W. / Tonge, P.J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors.
Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / ...Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionJan 10, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,96430
Polymers184,3576
Non-polymers6,60824
Water4,035224
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,40120
Polymers122,9054
Non-polymers4,49616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20130 Å2
ΔGint-195 kcal/mol
Surface area33520 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,12720
Polymers122,9054
Non-polymers4,22316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area20270 Å2
ΔGint-208 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.920, 130.359, 176.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11D-432-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23G
14A
24C
15A
25D
16B
26E
17B
27G
18B
28C
19B
29D
110E
210G
111E
211C
112E
212D
113G
213C
114G
214D
115C
215D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 269 / Label seq-ID: 22 - 289

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22EC
13AA
23GD
14AA
24CE
15AA
25DF
16BB
26EC
17BB
27GD
18BB
28CE
19BB
29DF
110EC
210GD
111EC
211CE
112EC
212DF
113GD
213CE
114GD
214DF
115CE
215DF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

-
Protein , 1 types, 6 molecules ABEGCD

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 30726.131 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)

-
Non-polymers , 5 types, 248 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-XT5 / 5-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-(2-methylphenoxy)phenol


Mass: 321.373 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C19H19N3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris/HCl, pH 8.0; 2.5 M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.8→46.3 Å / Num. obs: 52514 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.587 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x23
Resolution: 2.8→46.3 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / SU B: 33.272 / SU ML: 0.309 / Cross valid method: FREE R-VALUE / ESU R Free: 0.351 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 2576 4.9 %RANDOM
Rwork0.20604 ---
obs0.20786 49906 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---1.01 Å2-0 Å2
3---0.97 Å2
Refinement stepCycle: 1 / Resolution: 2.8→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11976 0 443 224 12643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01912719
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212212
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.98417343
X-RAY DIFFRACTIONr_angle_other_deg1.0763.00228020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07551616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84123.908476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.516151992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3851579
X-RAY DIFFRACTIONr_chiral_restr0.0880.21964
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114950
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022809
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_it0.6362.2486452
X-RAY DIFFRACTIONr_mcbond_other0.632.2466439
X-RAY DIFFRACTIONr_mcangle_it0.9983.378049
X-RAY DIFFRACTIONr_mcangle_other0.9943.3698044
X-RAY DIFFRACTIONr_scbond_it0.6572.3566264
X-RAY DIFFRACTIONr_scbond_other0.6572.3566265
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0383.5189265
X-RAY DIFFRACTIONr_long_range_B_refined1.97127.11613964
X-RAY DIFFRACTIONr_long_range_B_other1.97127.11613965
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)
11A161040.08
12B161040.08
21A162300.08
22E162300.08
31A162640.07
32G162640.07
41A164760.05
42C164760.05
51A161940.08
52D161940.08
61B163380.06
62E163380.06
71B163900.06
72G163900.06
81B161200.07
82C161200.07
91B163400.06
92D163400.06
101E164540.06
102G164540.06
111E161900.07
112C161900.07
121E165520.05
122D165520.05
131G162240.07
132C162240.07
141G164260.05
142D164260.05
151C161520.08
152D161520.08
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 203 -
Rwork0.305 3581 -
obs--99.19 %
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)
11.85590.6892-0.27541.4715-0.26621.6640.12230.31920.145-0.3678-0.1518-0.0095-0.08320.07340.02950.27130.0863-0.04760.2059-0.01170.119336.2584-36.3657-78.0432
20.95790.0422-0.64350.4313-0.06110.9956-0.00730.2846-0.0259-0.1565-0.05960.04330.0024-0.10430.06690.14230.0465-0.10760.1261-0.03740.10728.4341-41.5802-64.9981
31.43050.36690.3180.8705-0.02710.9728-0.01380.09710.2508-0.0987-0.0187-0.1415-0.1816-0.01820.03260.17320.0391-0.03890.0630.00870.146939.3218-30.1847-58.2714
40.46040.06520.15712.72080.47262.76370.0315-0.0333-0.07230.1867-0.03630.1607-0.0213-0.00050.00480.1228-0.02930.00780.19220.01190.18878.7161-48.3856-31.733
54.07831.18672.41880.8326-0.3664.74760.0704-0.16060.02840.00220.01980.22020.4502-0.4265-0.09020.1935-0.01630.05720.19270.00440.33580.5502-52.3035-37.792
62.872-1.63131.661.4173-2.12783.83970.0845-0.31610.0035-0.17080.18120.14260.3795-0.1736-0.26570.1014-0.0683-0.02260.2105-0.05430.30690.5734-46.9471-40.1819
71.4527-1.4877-0.37263.04640.69571.21940.0762-0.01-0.1055-0.1041-0.08060.3273-0.2101-0.24620.00440.0633-0.004-0.0390.1867-0.01380.25033.5121-39.7665-42.5072
80.71370.30480.12030.5054-0.38950.6638-0.01040.0778-0.1354-0.06040.04440.03440.0965-0.1574-0.03390.0731-0.0329-0.05050.1712-0.10210.223816.7433-46.361-50.5062
92.45670.1525-0.93180.0273-0.1941.42070.00420.093-0.17330.0036-0.0009-0.00890.0274-0.0637-0.00330.1146-0.0089-0.10190.0577-0.01670.109219.2432-44.0356-44.8341
101.57061.65760.91321.88970.9470.53330.12950.0759-0.3516-0.09010.0646-0.31150.0930.0373-0.19410.35250.011-0.03470.3553-0.09220.347724.526-64.7795-45.9456
112.02030.0639-1.36733.1278-0.91131.5422-0.216-0.1169-0.21290.07930.15370.03870.2516-0.14610.06230.1192-0.0145-0.06270.12220.00750.116424.335-49.3825-33.5217
122.3496-0.4556-0.27371.48740.56011.3321-0.0318-0.46950.15220.3137-0.00570.03350.0597-0.03410.03760.22650.0239-0.07750.2586-0.01310.07635.0519-36.2812-11.5821
130.1441-0.72910.08673.7766-0.51120.4161-0.0507-0.00980.03540.1615-0.0641-0.1324-0.06540.02590.11480.2070.0276-0.05030.27240.00930.162944.6394-48.078-8.9127
141.65050.1308-1.2590.3255-0.42911.4594-0.0223-0.3530.15940.1430.0851-0.1076-0.01020.0973-0.06280.17240.0325-0.12080.1895-0.05120.128547.2512-39.8367-23.5451
151.462-0.1445-0.6830.04290.12051.5992-0.1028-0.26430.03030.0352-0.00970.015-0.0225-0.01540.11250.12180.0176-0.07880.085-0.04810.106139.4229-40.4829-29.0068
164.35190.70892.50283.17810.51541.4871-0.24730.10960.26420.00280.11310.0421-0.22780.07870.13420.19820.0053-0.0110.1713-0.00820.183342.4179-19.6229-32.521
172.2387-0.594-0.70770.35690.76991.9552-0.0027-0.19240.079-0.029-0.0015-0.0121-0.1445-0.05930.00420.15960.0253-0.06590.0572-0.04790.06328.1038-34.6276-31.4299
180.7410.1551-0.13932.73680.40220.7517-0.00780.1172-0.0665-0.14450.0096-0.1550.0149-0.0451-0.00180.11950.02430.00690.1665-0.01520.197463.4913-46.3269-57.7824
191.7654-0.42830.86270.24010.31082.5359-0.0626-0.0270.040.04790.0408-0.05450.13790.0670.02180.1423-0.00140.01430.1672-0.00150.256771.7647-49.6003-51.6732
201.66741.58420.79632.3157-0.34254.17760.11390.12530.00550.1693-0.0232-0.3897-0.31110.5008-0.09070.06280.00990.03020.155-0.01430.374272.0414-39.4293-47.4952
210.6926-0.3703-0.22710.31110.47911.3984-0.0683-0.08690.05030.05480.0725-0.08990.07850.069-0.00420.07260.0204-0.03260.1191-0.03470.267659.4767-43.3394-39.0875
221.87190.1171-1.2872.54480.07941.9469-0.05840.0298-0.053-0.16780.0284-0.05060.15530.03040.030.07890.0318-0.07980.0486-0.04210.139252.1285-43.3746-45.2896
232.8638-0.15493.07961.8332-1.10893.80070.247-0.1359-0.08190.1973-0.03810.09660.2385-0.1607-0.20890.31520.0514-0.01280.32740.00890.307950.3311-64.0367-40.6808
242.1547-0.80440.2031.18050.91331.8041-0.08820.0565-0.2284-0.05050.0190.03260.10340.11620.06920.10570.04920.0090.0578-0.05190.142247.2484-49.7751-55.3554
250.5780.01530.85373.43110.37091.58910.05290.09920.06770.0093-0.050.28920.0148-0.0114-0.00290.10480.00950.03340.2075-0.02720.202815.65218.33530.486
260.7451-0.76310.28140.82190.05763.7964-0.14150.0141-0.0690.1001-0.06330.1355-0.1371-0.00650.20480.1613-0.04840.04340.2142-0.05630.261910.879911.67729.7635
270.9165-0.12961.68261.5403-1.39154.05290.1453-0.10480.04440.0286-0.10720.21940.145-0.1727-0.03820.1363-0.01680.03370.2112-0.04620.19312.05546.426811.3729
284.25411.67534.04022.31851.58475.64420.2153-0.0901-0.18250.088-0.07490.1566-0.0446-0.1702-0.14040.172-0.0440.04750.1911-0.00220.193512.4966-3.139415.4806
293.08770.93411.71971.14251.00591.29660.0778-0.3220.07960.1162-0.1210.2050.0111-0.15860.04320.1777-0.09370.13150.1997-0.03270.146627.36095.108515.5279
304.91642.42860.93913.82010.34511.06250.1303-0.04410.02070.1455-0.02720.0241-0.0511-0.08-0.10310.11330.03380.06560.061-0.00070.057231.74996.23715.0933
312.5402-0.15610.71560.0136-0.09390.84030.124-0.12230.0522-0.0027-0.02490.0042-0.0152-0.0446-0.09910.1419-0.04320.06670.0932-0.01520.036631.05714.29497.4554
321.6309-1.2447-1.2262.32210.67133.20730.1221-0.11450.20430.08140.0649-0.0794-0.05320.0054-0.1870.18-0.04780.02950.1688-0.02340.201733.35826.3969.2726
332.1891-0.18660.08781.0581-0.22731.70750.11530.0120.2961-0.2133-0.14140.1762-0.1238-0.0970.0260.1240.05050.01760.0672-0.02590.117931.382711.1623-4.5914
342.66490.65450.24173.5979-0.37852.03670.098-0.1772-0.21580.3521-0.2061-0.56140.10730.19860.10820.127-0.0672-0.05460.29110.06110.096664.2566-1.763924.2153
352.1737-1.4404-1.95741.54470.9212.0113-0.2339-0.2295-0.16840.49390.07450.05690.02020.22310.15930.3054-0.1337-0.07630.42480.03740.138559.8085-5.176133.7313
361.67790.1376-0.49662.30511.28771.5635-0.0609-0.50750.14940.4169-0.07070.12850.01520.20730.13160.2442-0.0839-0.02380.4124-0.01760.07255.89694.791334.9089
372.50020.02050.76920.21930.14580.57150.0959-0.3931-0.07530.13-0.1143-0.00540.0638-0.02740.01840.2447-0.09230.00450.2280.03540.037546.61331.005121.4792
382.6293-0.26780.77940.06970.15391.51270.046-0.24760.0259-0.00190.0609-0.0260.00940.0334-0.1070.1347-0.06480.03990.14040.00440.041849.29192.213216.4439
393.0705-0.2046-2.50472.6247-1.10033.138-0.06470.0271-0.27180.0697-0.162-0.0036-0.1629-0.19870.22670.3238-0.0845-0.03550.2530.03620.219144.9269-19.17914.418
402.0189-1.01160.1280.7961-0.65312.05530.0862-0.1691-0.2085-0.0079-0.04720.01650.13690.0556-0.0390.1466-0.054-0.03830.12970.06750.123158.5851-4.61578.6955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 67
2X-RAY DIFFRACTION2A68 - 202
3X-RAY DIFFRACTION3A203 - 269
4X-RAY DIFFRACTION4B2 - 31
5X-RAY DIFFRACTION5B32 - 53
6X-RAY DIFFRACTION6B54 - 67
7X-RAY DIFFRACTION7B68 - 99
8X-RAY DIFFRACTION8B100 - 158
9X-RAY DIFFRACTION9B159 - 201
10X-RAY DIFFRACTION10B202 - 225
11X-RAY DIFFRACTION11B226 - 269
12X-RAY DIFFRACTION12E2 - 67
13X-RAY DIFFRACTION13E68 - 82
14X-RAY DIFFRACTION14E83 - 137
15X-RAY DIFFRACTION15E138 - 201
16X-RAY DIFFRACTION16E202 - 221
17X-RAY DIFFRACTION17E222 - 269
18X-RAY DIFFRACTION18G2 - 31
19X-RAY DIFFRACTION19G32 - 53
20X-RAY DIFFRACTION20G54 - 82
21X-RAY DIFFRACTION21G83 - 137
22X-RAY DIFFRACTION22G138 - 201
23X-RAY DIFFRACTION23G202 - 221
24X-RAY DIFFRACTION24G222 - 269
25X-RAY DIFFRACTION25C2 - 31
26X-RAY DIFFRACTION26C32 - 53
27X-RAY DIFFRACTION27C54 - 67
28X-RAY DIFFRACTION28C68 - 82
29X-RAY DIFFRACTION29C83 - 137
30X-RAY DIFFRACTION30C138 - 158
31X-RAY DIFFRACTION31C159 - 201
32X-RAY DIFFRACTION32C202 - 221
33X-RAY DIFFRACTION33C222 - 269
34X-RAY DIFFRACTION34D2 - 31
35X-RAY DIFFRACTION35D32 - 53
36X-RAY DIFFRACTION36D54 - 82
37X-RAY DIFFRACTION37D83 - 158
38X-RAY DIFFRACTION38D159 - 201
39X-RAY DIFFRACTION39D202 - 221
40X-RAY DIFFRACTION40D222 - 269

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more