[English] 日本語
Yorodumi
- PDB-4my9: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4my9
TitleCrystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor C91
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / alpha-beta structure / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-C91 / INOSINIC ACID / MALONATE ION / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5893 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Gorla, S.K. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor C91
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,40833
Polymers325,6778
Non-polymers6,73125
Water5,585310
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,35718
Polymers162,8384
Non-polymers3,51914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25190 Å2
ΔGint-114 kcal/mol
Surface area46340 Å2
MethodPISA
2
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,05115
Polymers162,8384
Non-polymers3,21311
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24470 Å2
ΔGint-119 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.930, 89.883, 104.621
Angle α, β, γ (deg.)98.70, 90.32, 96.46
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 40709.574 Da / Num. of mol.: 8 / Fragment: IMPDH-delt-L-CBS / Mutation: replaced residues 92-220 with GG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: guaB, BA_0008, BAS0011, GBAA_0008 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81W29, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase
#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-C91 / N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide


Mass: 378.426 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H18N4O
#4: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5 % w/v Tacsimate, 0.1 M HEPES, pH 7.0, 10% w/v PEGMME 5000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.589→50 Å / Num. all: 91462 / Num. obs: 91462 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 46.8 Å2 / Rsym value: 0.081 / Net I/σ(I): 11.1
Reflection shellResolution: 2.589→2.64 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4515 / Rsym value: 0.407 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID ENTRY 3STD
Resolution: 2.5893→38.748 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4583 5.02 %random
Rwork0.17 ---
all0.172 91344 --
obs0.172 91344 96.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5893→38.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20464 0 479 310 21253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321280
X-RAY DIFFRACTIONf_angle_d0.7428803
X-RAY DIFFRACTIONf_dihedral_angle_d13.9827796
X-RAY DIFFRACTIONf_chiral_restr0.0463327
X-RAY DIFFRACTIONf_plane_restr0.0033700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5893-2.61880.3478780.31241613169154
2.6188-2.64960.33851680.26762962313097
2.6496-2.68190.30721470.25712855300298
2.6819-2.71580.3011770.25182929310698
2.7158-2.75150.2981720.24672890306298
2.7515-2.78920.3321560.24872905306198
2.7892-2.8290.31161560.23732996315297
2.829-2.87130.29111340.23112884301898
2.8713-2.91610.31221790.22342894307398
2.9161-2.96390.29321440.22642924306498
2.9639-3.0150.2821470.22292955310298
3.015-3.06980.27671450.22332977312298
3.0698-3.12880.2941540.21142897305198
3.1288-3.19260.26621650.20392931309698
3.1926-3.2620.23111490.19312958310798
3.262-3.33790.27281530.18622912306598
3.3379-3.42130.23041690.19192908307798
3.4213-3.51370.20781530.17292965311898
3.5137-3.61710.25431610.17912927308898
3.6171-3.73370.21721530.16242950310398
3.7337-3.86710.1991510.16212972312399
3.8671-4.02170.20731380.15192920305898
4.0217-4.20460.20291650.1392957312299
4.2046-4.42590.15951350.1336293830798
4.4259-4.70280.15771690.12822986315599
4.7028-5.06520.16131440.11982948309299
5.0652-5.57360.17431720.13862934310699
5.5736-6.3770.19091580.15012977313599
6.377-8.02260.15021350.14232971310699
8.0226-38.75210.15461560.14062926308298
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)
10.5651-0.15380.16521.09370.12120.8138-0.05170.04050.0248-0.15940.03820.1821-0.0385-0.15970.02130.3459-0.0225-0.03350.32460.03580.22681.94465.4019-2.0165
20.9503-0.15020.18691.0122-0.27621.21640.02340.045-0.2071-0.2065-0.0640.1720.1078-0.21190.01360.3593-0.0486-0.03960.3407-0.03210.29780.7559-4.4139-4.5226
34.8518-1.59040.10191.28520.07831.3796-0.4799-0.5997-0.30830.4990.35460.2370.0003-0.09010.19860.3580.00480.07310.38750.06610.2928-0.1524-3.318417.1511
40.74340.3662-0.02531.3663-0.06831.30390.03650.0143-0.1079-0.184-0.02980.1239-0.1707-0.1380.01180.36680.0485-0.03280.2706-0.01010.2525.19718.56113.8158
51.74271.1861.03981.84710.83921.2071-0.17610.0768-0.0817-0.39680.0917-0.3062-0.27480.21830.12520.4113-0.03320.09010.28750.0580.293325.901524.8597-1.082
62.58540.483-0.50041.3748-0.1121.25530.0035-0.04750.5353-0.19830.00790.1775-0.2530.1740.02350.48880.03710.08350.3030.01360.390819.231346.265810.9014
71.7356-0.4694-0.05071.7729-0.27641.80430.2624-0.00070.00660.07750.01530.4237-0.6463-0.4176-0.25970.67580.16150.04860.32360.03820.47293.394748.996812.3261
80.5581-0.43240.07181.51020.4180.2117-0.04580.14150.1541-0.4040.14410.3777-0.3122-0.19-0.09890.69870.0802-0.0370.33760.07980.35366.183142.2679-3.3948
90.72220.2065-0.14780.8397-0.14990.5379-0.0440.07950.092-0.11740.1022-0.0173-0.3992-0.1427-0.07470.45230.00970.02210.2630.03210.283517.692133.39383.4854
101.73810.5491-0.30751.90590.25141.57880.1887-0.0265-0.03160.2765-0.12690.1376-0.1917-0.17060.00820.41450.02380.05990.28430.0180.27186.962932.950923.6048
111.59150.7877-0.37081.44781.19841.62890.1566-0.25880.26920.0198-0.14540.1951-0.15740.02970.01980.42720.0393-0.02280.18870.06670.306917.456435.335817.8504
121.3710.34390.51231.38850.39281.1167-0.07370.11790.0154-0.01260.0948-0.0297-0.1782-0.0172-0.04090.3052-0.02880.05020.25490.04630.287631.308629.456613.8752
131.69160.7587-0.05190.6707-0.12050.3986-0.03450.0867-0.198-0.1650.0222-0.291-0.07640.10680.00470.31860.02320.03240.24340.0150.220332.20920.5808-0.2493
140.93230.01320.24021.32580.04981.51720.0598-0.068-0.19880.32250.0682-0.28460.39520.2011-0.13720.53150.0926-0.02720.2850.00930.406938.381-24.683416.9596
150.18720.6988-0.05962.6023-0.21740.1102-0.112-0.0474-0.04550.22660.2003-0.54480.03510.1639-0.09250.39750.10210.02950.3935-0.03630.602751.2159-17.054411.4406
160.32940.43340.25740.903-0.03120.6638-0.0613-0.0703-0.1506-0.08990.0642-0.1380.0410.1795-0.01850.36230.04620.05090.3064-0.04280.345440.4571-10.30026.6834
171.07180.54490.33661.6944-0.09431.1330.1591-0.2133-0.06250.384-0.08030.00730.2802-0.0046-0.01770.38050.00710.02210.23040.0120.274428.6125-12.561721.6897
181.3428-0.10710.3250.8838-0.31331.5831-0.0571-0.00780.03070.22030.0924-0.0882-0.0468-0.152-0.00780.3538-0.0215-0.01410.257-0.01340.249219.1976-5.45766.1399
190.8387-0.06950.00270.69520.14170.7891-0.05370.01570.03960.09830.0441-0.2707-0.13870.2102-0.02460.2694-0.0299-0.02240.3230.01250.384350.202718.830718.4363
201.1918-0.20380.27881.27250.30670.0996-0.01430.02030.12520.12840.0542-0.399-0.22760.247-0.01640.3649-0.1115-0.02070.3656-0.00780.431852.306929.954218.4516
211.8439-0.95590.33811.2163-0.27930.9654-0.3181-0.3343-0.15530.45340.17240.0135-0.11080.01540.1750.4746-0.0746-0.02260.3415-0.02320.371442.193218.863332.8535
221.242-0.09340.54940.9119-0.39971.6868-0.0665-0.30410.07150.35150.0888-0.166-0.26110.14320.05110.3775-0.0672-0.04360.297-0.00280.380743.630218.034127.441
231.3286-0.3490.23431.86790.48441.42130.08450.10650.1520.005-0.0581-0.2569-0.11540.0193-0.04020.27580.01520.0180.2296-0.00670.287741.69285.023815.863
240.84380.00310.0480.25320.1780.8298-0.06230.19740.0872-0.15680.0189-0.1030.1608-0.03260.03060.42440.05570.05370.35710.07670.23974.910113.462549.6864
251.1946-0.3690.06662.66120.81991.6641-0.041-0.16990.24260.40710.0237-0.50490.14380.58110.0580.30510.01250.00140.42720.00710.44924.107123.798561.0387
261.1883-0.1413-0.34550.20390.00070.83940.07010.14060.3001-0.0906-0.1245-0.1977-0.10110.1590.050.43250.04690.04570.40550.10530.37528.647124.971452.0512
273.0296-0.2089-0.25611.42470.08652.3318-0.2266-0.40850.05130.80060.0757-0.22450.40460.23130.10060.51220.0432-0.0190.45570.04220.365311.60117.329973.3783
281.3129-0.15710.38481.14640.39380.87010.05740.02740.0306-0.0988-0.0132-0.13010.06390.0026-0.02790.41110.0880.06850.34840.01180.26865.65240.880654.1248
291.44030.6246-0.04771.31-0.03170.5346-0.15180.20360.1726-0.28340.06920.18030.0581-0.0790.04220.42950.05590.00370.35010.08620.307-21.827319.209355.2671
301.4880.03070.02811.3982-0.1171.1679-0.0561-0.19310.25360.26050.00250.2172-0.224-0.1870.0070.51390.11160.07940.3576-0.02050.4215-25.021238.578979.0744
310.42640.4538-0.1811.22720.36080.34320.00360.03280.14020.0363-0.03090.2911-0.1846-0.25440.01350.39720.15870.06060.37710.06410.3987-31.900130.413968.1307
321.39540.07030.68152.28861.10521.34050.0958-0.15920.0440.55250.1543-0.24260.1646-0.2987-0.13650.45280.07050.00070.43390.00680.3588-18.849322.675587.1401
331.00040.018-0.01530.9440.2411.80010.0763-0.1919-0.03840.1054-0.21850.0772-0.25710.1410.0540.32910.06890.00830.1861-0.0160.2964-14.881527.422476.2438
341.40560.381-0.01030.92370.20811.1122-0.06660.03490.01340.15840.00740.15510.06050.14020.08880.34010.07660.04530.29840.06710.2688-7.962723.385163.4032
351.82711.06730.08291.77-0.27480.3728-0.05460.0471-0.025-0.22-0.0434-0.07560.0092-0.03870.04390.43550.1186-0.03940.3183-0.03440.2515-14.5763-3.0447.1342
361.4678-0.3125-0.13771.0238-0.30591.5778-0.174-0.0915-0.3402-0.28380.0725-0.24260.43140.21980.05310.52960.07850.02710.2907-0.03870.3811-0.3072-29.779354.2756
370.0877-0.13540.21761.4789-0.43830.68210.09150.1831-0.0982-0.2585-0.1131-0.21780.42430.2952-0.01860.64850.15530.12610.5496-0.04950.43289.4918-24.50945.3367
380.3388-0.11790.19461.85160.14010.41610.03650.1613-0.1208-0.3549-0.0269-0.02340.21890.06510.00250.55970.04990.02610.4229-0.03270.2851-3.1155-15.414946.1997
390.6220.366-0.32313.3037-1.37592.4717-0.0119-0.244-0.18270.2382-0.2286-0.44730.01620.27460.27590.37840.0892-0.00590.3537-0.01610.33055.075-17.056167.9572
401.5272-0.0035-0.19611.587-0.23270.3656-0.09290.0461-0.0572-0.01840.10640.16850.22630.039-0.05570.375-0.0043-0.00950.31010.00690.2667-19.7911-15.818360.4686
411.0348-0.2133-0.17190.85940.20770.41540.12680.1740.051-0.182-0.1810.1317-0.2195-0.35730.06410.37390.1148-0.00630.48270.06990.4911-36.09773.678659.581
421.1578-0.19110.27751.13790.34811.02220.022-0.1511-0.15320.25650.04520.30850.2821-0.3059-0.02370.457-0.09040.08560.48660.0330.4864-45.553-16.655176.5404
430.6265-0.1147-0.66640.2014-0.07880.9174-0.01510.1442-0.23540.0536-0.09930.1540.20690.0240.14280.4832-0.1027-0.02690.5761-0.07760.6323-44.3269-20.54961.3362
440.51-0.08060.14980.9093-0.0570.8612-0.02590.15640.1314-0.0599-0.07880.28580.2692-0.27190.11830.3098-0.0364-0.00160.45420.00470.3468-37.5328-7.507560.7807
452.1955-0.6314-1.68831.93450.43271.5104-0.2112-0.5827-0.12990.38160.08970.11890.15730.3018-0.01790.5223-0.03830.03530.47050.01380.3539-31.3257-7.572381.7065
461.1442-0.2484-0.8521.08841.03012.5941-0.0788-0.1073-0.20890.37180.0306-0.0010.45990.176-0.01930.56720.0240.01660.38690.0220.3878-26.9046-15.98577.2408
470.46590.2017-0.27791.5039-0.10521.1379-0.06880.011-0.05920.1528-0.06220.1941-0.0052-0.12460.12270.28980.02580.06170.35570.03120.327-33.55829.805771.6211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 368 )
3X-RAY DIFFRACTION3chain 'A' and (resid 369 through 427 )
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 486 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 56 )
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 242 )
8X-RAY DIFFRACTION8chain 'B' and (resid 243 through 293 )
9X-RAY DIFFRACTION9chain 'B' and (resid 294 through 363 )
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 400 )
11X-RAY DIFFRACTION11chain 'B' and (resid 401 through 446 )
12X-RAY DIFFRACTION12chain 'B' and (resid 447 through 486 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 26 )
14X-RAY DIFFRACTION14chain 'C' and (resid 27 through 242 )
15X-RAY DIFFRACTION15chain 'C' and (resid 243 through 268 )
16X-RAY DIFFRACTION16chain 'C' and (resid 269 through 355 )
17X-RAY DIFFRACTION17chain 'C' and (resid 356 through 446 )
18X-RAY DIFFRACTION18chain 'C' and (resid 447 through 486 )
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 77 )
20X-RAY DIFFRACTION20chain 'D' and (resid 78 through 355 )
21X-RAY DIFFRACTION21chain 'D' and (resid 356 through 389 )
22X-RAY DIFFRACTION22chain 'D' and (resid 390 through 446 )
23X-RAY DIFFRACTION23chain 'D' and (resid 447 through 486 )
24X-RAY DIFFRACTION24chain 'E' and (resid -2 through 56 )
25X-RAY DIFFRACTION25chain 'E' and (resid 57 through 90 )
26X-RAY DIFFRACTION26chain 'E' and (resid 91 through 368 )
27X-RAY DIFFRACTION27chain 'E' and (resid 369 through 427 )
28X-RAY DIFFRACTION28chain 'E' and (resid 428 through 486 )
29X-RAY DIFFRACTION29chain 'F' and (resid -1 through 26 )
30X-RAY DIFFRACTION30chain 'F' and (resid 27 through 232 )
31X-RAY DIFFRACTION31chain 'F' and (resid 233 through 363 )
32X-RAY DIFFRACTION32chain 'F' and (resid 364 through 398 )
33X-RAY DIFFRACTION33chain 'F' and (resid 399 through 446 )
34X-RAY DIFFRACTION34chain 'F' and (resid 447 through 486 )
35X-RAY DIFFRACTION35chain 'G' and (resid -2 through 26 )
36X-RAY DIFFRACTION36chain 'G' and (resid 27 through 230 )
37X-RAY DIFFRACTION37chain 'G' and (resid 231 through 257 )
38X-RAY DIFFRACTION38chain 'G' and (resid 258 through 368 )
39X-RAY DIFFRACTION39chain 'G' and (resid 369 through 427 )
40X-RAY DIFFRACTION40chain 'G' and (resid 428 through 486 )
41X-RAY DIFFRACTION41chain 'H' and (resid -1 through 39 )
42X-RAY DIFFRACTION42chain 'H' and (resid 40 through 242 )
43X-RAY DIFFRACTION43chain 'H' and (resid 243 through 270 )
44X-RAY DIFFRACTION44chain 'H' and (resid 271 through 355 )
45X-RAY DIFFRACTION45chain 'H' and (resid 356 through 389 )
46X-RAY DIFFRACTION46chain 'H' and (resid 390 through 427 )
47X-RAY DIFFRACTION47chain 'H' and (resid 428 through 486 )

+
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