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- PDB-5ugt: Crystal structure of M. tuberculosis InhA inhibited by PT504 -

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Basic information

Entry
Database: PDB / ID: 5ugt
TitleCrystal structure of M. tuberculosis InhA inhibited by PT504
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-XTW / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,92512
Polymers122,9054
Non-polymers4,0218
Water2,396133
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19010 Å2
ΔGint-131 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.924, 92.785, 180.426
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23G
14B
24E
15B
25G
16E
26G

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 2 - 269 / Label seq-ID: 22 - 289

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22EC
13AA
23GD
14BB
24EC
15BB
25GD
16EC
26GD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 341.792 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H16ClN3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.1 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2 M sodium acetate, pH 7.0

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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: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.6→46.58 Å / Num. obs: 43766 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.089 / Net I/σ(I): 7.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.6 % / Num. unique obs: 4566 / CC1/2: 0.299 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x23
Resolution: 2.6→46.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 35.777 / SU ML: 0.339 / Cross valid method: FREE R-VALUE / ESU R: 0.562 / ESU R Free: 0.285 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23947 2159 4.9 %RANDOM
Rwork0.21066 ---
obs0.21213 41604 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.339 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0 Å20.2 Å2
2---0.51 Å20 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.6→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 272 133 8321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198380
X-RAY DIFFRACTIONr_bond_other_d0.0030.028043
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.9811420
X-RAY DIFFRACTIONr_angle_other_deg1.1393.00218459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80351061
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23823.885314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.624151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0821552
X-RAY DIFFRACTIONr_chiral_restr0.1030.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219818
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021850
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_it1.4382.54252
X-RAY DIFFRACTIONr_mcbond_other1.4262.4944243
X-RAY DIFFRACTIONr_mcangle_it2.4313.7395300
X-RAY DIFFRACTIONr_mcangle_other2.4193.7355297
X-RAY DIFFRACTIONr_scbond_it1.8092.7844128
X-RAY DIFFRACTIONr_scbond_other1.8092.7854129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7874.1366106
X-RAY DIFFRACTIONr_long_range_B_refined6.04630.5879244
X-RAY DIFFRACTIONr_long_range_B_other6.04230.5399234
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)
11A159240.05
12B159240.05
21A164280.06
22E164280.06
31A159360.06
32G159360.06
41B159600.05
42E159600.05
51B159180.06
52G159180.06
61E160300.07
62G160300.07
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 148 -
Rwork0.391 3076 -
obs--98.23 %
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)
15.1658-0.7191-0.823.2278-0.19365.7789-0.0387-0.6611-0.52720.4430.2184-0.39530.74560.2405-0.17970.73950.08730.22060.11760.13150.843-26.662-3.5257-24.8315
28.0148-1.12745.40552.758-0.47813.68250.75770.6116-0.8507-0.554-0.25590.12560.41530.4185-0.50170.8620.05230.150.30590.07630.9838-27.2198-11.9067-32.0046
34.48892.00141.54935.3703-1.76296.413-0.0904-0.1968-0.5062-0.19090.13270.45450.8374-0.5485-0.04240.7771-0.03410.12270.2070.0790.8133-37.7471-11.7407-31.0636
42.617-0.51461.28253.4085-1.48281.583-0.146-0.1035-0.6132-0.41170.29340.42980.6636-0.1757-0.14740.7182-0.05480.28610.02960.01680.7815-38.2344.5206-36.9241
55.4296-0.16173.13383.0775-0.74932.15660.2868-0.0773-0.6809-0.265-0.18170.0762-0.10530.2433-0.10510.6777-0.17860.18510.28090.26590.7332-28.26055.6219-33.1022
63.0975-0.7572-4.69730.63760.42258.4680.19350.3535-0.2918-0.4634-0.32090.39760.38670.28450.12750.85870.01670.11261.068-0.01230.9767-19.00110.7183-47.0693
71.1469-3.3838-0.748310.23272.26890.50610.26630.01440.0563-0.8979-0.1856-0.4231-0.188-0.0259-0.08070.4410.14150.10140.41380.09720.5785-16.693412.7248-32.9608
82.0382-1.94381.84034.6686-0.17062.56390.1939-0.2254-0.09340.46790.1201-0.4850.5651-0.2487-0.3140.42750.09110.1930.12920.13220.6785-28.222412.2205-25.556
93.0301-1.6731-0.55175.096-1.78913.0221-0.03240.61380.0815-0.6540.23320.86990.0315-0.4935-0.20080.6069-0.2041-0.2390.47160.08130.8376-54.905730.8663-57.0306
100.4056-0.1549-0.72654.16521.62431.8387-0.12630.5363-0.0519-0.54990.02750.57540.3084-0.91860.09880.8991-0.3005-0.38840.73330.02861.1493-59.715822.1707-61.5538
111.75910.8139-1.174.1486-1.99453.7613-0.02580.5499-0.603-1.3366-0.27140.45410.83630.09440.29720.9314-0.1275-0.24770.6071-0.05860.9242-48.65718.9965-63.2335
121.4315-0.58661.68274.4337-0.37032.03910.077-0.2419-0.3273-0.87020.27771.04140.1988-0.3633-0.35470.67-0.3460.03350.32680.06170.9266-48.895510.1149-48.1133
133.39740.8586-3.44154.3687-3.46376.68220.1281-0.11320.0828-0.59720.31761.07190.42750.3382-0.44570.2879-0.12870.01650.2854-0.01170.6229-46.073722.7642-45.1261
142.2827-1.92351.81083.38180.00062.80310.3240.1506-0.4474-0.4564-0.08640.58020.17110.0816-0.23760.3942-0.15480.05930.12690.0080.6178-40.167817.4509-47.6624
158.02255.8872-7.31364.5688-4.97367.4461-0.46081.34381.0213-0.36930.96530.84330.597-1.3596-0.50450.3362-0.10490.08360.30950.04830.6619-45.533127.2857-48.2853
160.4501-2.4505-0.170624.4509-10.400211.7444-0.01580.0919-0.03130.1372-0.3880.0692-0.0287-0.2240.40370.4364-0.1042-0.04520.54290.05960.7767-62.45518.8479-42.0918
171.3552.79710.75897.8173-3.943916.1034-0.33420.0821-0.0378-0.94150.66850.0713-0.1758-0.5765-0.33430.7515-0.0631-0.01580.89140.09560.7419-63.843520.1195-30.709
183.23063.0448-1.77983.0795-1.98696.24060.2909-0.43690.09190.2614-0.18540.40840.6479-0.6041-0.10550.3499-0.04110.06150.60520.06560.7571-56.920730.5398-34.4344
190.00630.0501-0.02572.92340.66761.16270.0210.03980.0211-0.52080.22840.1361-0.1404-0.3802-0.24940.33480.0206-0.03520.42320.0550.5567-45.483834.5926-50.7128
207.82131.60236.56822.79662.43856.0007-0.1518-0.52140.09350.4809-0.30580.92030.1131-0.53320.45760.2118-0.04360.21260.26830.11220.6307-46.040930.1884-35.3365
213.0327-0.27920.34364.5752-0.97983.9539-0.18350.13170.7346-0.16890.13720.2493-0.5629-0.08160.04630.26670.04190.09870.06090.01220.6005-35.188356.401-41.3084
221.5412-0.3233-0.29424.1862-0.75182.8371-0.3509-0.26330.30350.68190.271-0.0153-0.26170.05890.07990.29230.08450.13680.0578-0.05280.4847-31.74842.258-29.9061
239.4069-0.78462.51893.3429-0.17762.4187-0.03290.54590.2878-0.05780.0607-0.0822-0.13220.19-0.02780.2672-0.0370.11670.07010.05960.3427-31.072942.5649-41.4879
240.4936-0.5638-1.13447.69744.58834.1524-0.0025-0.064-0.1478-0.4534-0.42550.4692-0.1748-0.04750.4280.60940.0159-0.06370.65160.02040.7443-11.956438.695-40.116
251.2606-2.0629-0.46353.42710.77330.176-0.3643-0.21330.4170.64360.5059-0.57880.13460.1399-0.14160.657-0.02140.06830.72710.00280.6589-20.655931.6872-45.6709
260.65221.76630.25295.3979-0.45553.2522-0.19510.0821-0.0282-0.5870.0293-0.12640.0644-0.01290.16570.1730.00830.1410.22060.02570.4189-34.441435.4901-46.8148
271.34871.0111-0.18412.4979-0.89562.02740.0789-0.7445-0.43431.1937-0.1631-0.34250.19170.13680.08421.140.17630.0350.67320.13550.6658-26.399118.2527-5.23
281.68092.53080.37976.19011.86770.87140.2819-0.40240.21040.3673-0.2166-0.0751-0.0022-0.052-0.06530.82050.0531-0.04340.75580.00080.6023-25.83126.47052.2251
290.7510.45350.77690.31690.51630.86060.0517-0.3798-0.00610.1543-0.0708-0.00460.1208-0.20910.0191.17840.1375-0.06580.79680.01610.636-21.815228.3042-1.0521
303.9733-0.8739-0.03931.2555-0.71240.9351-0.0023-0.54960.38320.9276-0.2949-0.5999-0.26180.8090.29721.22360.0436-0.26380.85380.04480.7431-17.067929.3972-7.7784
312.4891-1.0651-0.52634.5091-0.45061.8252-0.1673-0.99560.52341.30780.1971-0.4745-0.0068-0.1414-0.02970.63760.05590.07940.5482-0.12840.4581-29.338738.9321-15.8595
320.8446-0.95160.28084.5402-1.3183.13560.0375-0.2848-0.15170.78940.0689-0.13050.1495-0.0067-0.10630.44550.02180.10980.25780.03760.4658-28.09527.545-21.0259
338.2743-5.83394.32976.2006-7.155910.93070.09050.071-0.26410.0824-0.040.4045-0.20910.0785-0.05050.628-0.03480.11150.5738-0.02380.5584-42.085930.3808-7.5271
340.12041.55510.687120.7349.20024.09460.0390.00260.0344-0.4244-0.25390.407-0.1876-0.23180.21480.7223-0.0360.07531.0160.06110.5998-51.445828.3898-14.5355
351.12371.1988-0.75832.4213-0.02325.33840.0419-0.4756-0.39680.6319-0.11090.13820.4032-0.21270.0690.63310.14620.39260.51230.38240.6772-35.559915.9385-15.7947
364.26230.72464.55327.84131.77955.0284-0.6175-0.55360.48120.72760.05310.3697-0.396-0.61340.56440.5554-0.0020.21980.33890.11260.4555-40.252619.3441-24.1447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 31
2X-RAY DIFFRACTION2A32 - 53
3X-RAY DIFFRACTION3A54 - 81
4X-RAY DIFFRACTION4A82 - 182
5X-RAY DIFFRACTION5A183 - 200
6X-RAY DIFFRACTION6A201 - 224
7X-RAY DIFFRACTION7A225 - 235
8X-RAY DIFFRACTION8A236 - 269
9X-RAY DIFFRACTION9B2 - 31
10X-RAY DIFFRACTION10B32 - 67
11X-RAY DIFFRACTION11B68 - 99
12X-RAY DIFFRACTION12B100 - 137
13X-RAY DIFFRACTION13B138 - 158
14X-RAY DIFFRACTION14B159 - 182
15X-RAY DIFFRACTION15B183 - 194
16X-RAY DIFFRACTION16B195 - 203
17X-RAY DIFFRACTION17B211 - 217
18X-RAY DIFFRACTION18B218 - 235
19X-RAY DIFFRACTION19B236 - 255
20X-RAY DIFFRACTION20B256 - 269
21X-RAY DIFFRACTION21E2 - 99
22X-RAY DIFFRACTION22E100 - 182
23X-RAY DIFFRACTION23E183 - 200
24X-RAY DIFFRACTION24E201 - 217
25X-RAY DIFFRACTION25E218 - 223
26X-RAY DIFFRACTION26E224 - 269
27X-RAY DIFFRACTION27G2 - 31
28X-RAY DIFFRACTION28G32 - 53
29X-RAY DIFFRACTION29G54 - 67
30X-RAY DIFFRACTION30G68 - 99
31X-RAY DIFFRACTION31G100 - 137
32X-RAY DIFFRACTION32G138 - 193
33X-RAY DIFFRACTION33G194 - 203
34X-RAY DIFFRACTION34G213 - 221
35X-RAY DIFFRACTION35G222 - 255
36X-RAY DIFFRACTION36G256 - 269

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