[English] 日本語
Yorodumi
- PDB-4my1: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4my1
TitleCrystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Bacillus anthracis str. Ames complexed with P68
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
INOSINIC ACID / Chem-P68 / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5997 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 a Internal Deletion of CBS Domain from Bacillus anthracis str. Ames complexed with P68
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 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)331,58424
Polymers325,6778
Non-polymers5,90816
Water2,108117
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)165,79212
Polymers162,8384
Non-polymers2,9548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23720 Å2
ΔGint-127 kcal/mol
Surface area47640 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)165,79212
Polymers162,8384
Non-polymers2,9548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23760 Å2
ΔGint-125 kcal/mol
Surface area47090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.220, 89.391, 103.987
Angle α, β, γ (deg.)81.13, 89.95, 83.59
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-delta-L-CBS / Mutation: CBS domain (residues 92-220) is replaced with GG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS0011, BA_0008, GBAA_0008, guaB / 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-P68 / 1-(4-bromophenyl)-3-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea


Mass: 390.274 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H20BrN3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M succinic acid pH 7.0, 15% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.5997→50 Å / Num. all: 88256 / Num. obs: 88256 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 45.76 Å2 / Rsym value: 0.09 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5997→2.64 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4394 / Rsym value: 0.426 / % possible all: 97.8

-
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 3TSD
Resolution: 2.5997→36.254 Å / SU ML: 0.36 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4415 5.01 %random
Rwork0.194 ---
all0.197 88200 --
obs0.197 88200 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5997→36.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20517 0 376 117 21010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921209
X-RAY DIFFRACTIONf_angle_d1.20828717
X-RAY DIFFRACTIONf_dihedral_angle_d17.7097719
X-RAY DIFFRACTIONf_chiral_restr0.0753338
X-RAY DIFFRACTIONf_plane_restr0.0053692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5997-2.62920.34891490.28182558270791
2.6292-2.66010.3291520.28192759291197
2.6601-2.69260.36431260.2942782290895
2.6926-2.72660.33741620.26862805296898
2.7266-2.76250.36231740.26162754292898
2.7625-2.80030.30751560.23982851300798
2.8003-2.84030.36171420.2372758290098
2.8403-2.88270.27061330.23232911304498
2.8827-2.92770.33351430.22992734287798
2.9277-2.97570.28961400.23312892303298
2.9757-3.0270.28521570.23262769292698
3.027-3.0820.30711700.22352837300798
3.082-3.14130.30941270.23122800292799
3.1413-3.20530.32021380.23352864301299
3.2053-3.2750.31671660.22362788295498
3.275-3.35110.27191420.21172831297398
3.3511-3.43490.28271430.20972772291597
3.4349-3.52770.24431280.20972785291397
3.5277-3.63140.30071460.2062847299398
3.6314-3.74850.24531550.19632745290097
3.7485-3.88230.25591560.19222803295898
3.8823-4.03750.25711400.17882787292797
4.0375-4.2210.21441590.16422771293098
4.221-4.44320.21361310.16722844297598
4.4432-4.7210.20921430.15962821296498
4.721-5.08460.22211530.15632763291697
5.0846-5.59470.20611690.16812800296998
5.5947-6.40040.20841570.17462816297398
6.4004-8.04920.17941190.15312817293698
8.0492-36.25740.19511390.15492721286095
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)
10.55890.1855-0.16531.77630.17320.6946-0.1248-0.00060.0493-0.10020.1689-0.2332-0.11890.1097-0.06040.47590.0374-0.06710.5278-0.00810.392519.0518-4.480914.5014
23.2707-0.04540.77832.344-0.25772.2055-0.16680.0594-0.30940.15130.1846-0.24190.42670.6594-0.00950.49540.1404-0.02370.6527-0.03440.507736.8846-20.71589.8361
33.3693-0.32970.390.2020.52660.8565-0.3299-0.337-0.46360.17980.0603-0.08710.24080.37620.27580.46120.07090.00660.50960.11920.488325.1157-24.671619.5416
42.2020.27310.59051.24020.06491.8241-0.18370.1129-0.0684-0.03040.0708-0.099-0.05680.32740.1040.34950.0049-0.01970.4508-0.00320.359621.0072-11.462110.1018
51.121-0.6233-0.1442.50290.7041.484-0.19030.17430.0132-0.03980.20090.03020.08850.2722-00.29550.0004-0.01020.45250.02260.391224.7048-8.68291.1945
62.2770.5294-0.04841.0026-0.17950.887-0.01390.02770.1104-0.0169-0.05780.02210.10820.1760.06530.5218-0.0104-0.07350.5098-0.07130.497116.40156.71556.1607
70.7232-0.23010.17140.71830.0011.51340.0899-0.08160.23730.04820.0112-0.0876-0.40780.1825-0.10560.4628-0.01980.02560.3729-0.07580.45189.349828.07281.5335
80.56740.1777-0.11941.4567-0.42420.14890.0763-0.12140.10230.17450.0265-0.1837-0.30480.2268-0.09680.5975-0.06420.01260.4544-0.07490.472414.481426.71448.3191
91.5773-0.4339-0.2060.7143-0.18792.04490.22690.37080.1725-0.1256-0.1410.01-0.20340.2309-0.07820.5043-0.03740.01110.332-0.02270.450713.693621.9128-11.0093
102.2728-0.75650.76292.2864-0.21051.80240.0220.0606-0.1164-0.18260.1089-0.2804-0.47730.2255-0.08180.521-0.02080.07410.39170.01480.4337-5.930317.3188-3.4412
111.4775-1.17871.51582.9276-0.99142.3106-0.1557-0.03430.15060.28190.13970.1771-0.1095-0.68840.08790.4159-0.0570.05590.50420.00050.3983-17.2222-4.51659.8713
121.46190.677-0.01281.6192-0.29463.47740.0261-0.0956-0.22250.0448-0.1886-0.12170.60.24330.14760.3720.01740.0430.33850.01190.4342-2.8066-32.87363.842
132.40830.74810.20762.88540.43192.9539-0.0470.3083-0.3234-0.27240.08530.18980.4308-0.4046-0.01740.4985-0.1025-0.06120.42780.01490.497-16.7015-38.0211-10.8439
141.3795-0.5984-0.23141.96320.95572.1663-0.15630.382-0.3170.1034-0.0180.42060.0853-0.740.16230.4512-0.08050.03530.7160.06210.614-26.2454-29.9239-1.3155
150.7529-0.7082-0.06540.80190.13441.2011-0.08660.0952-0.12280.11510.05430.15910.236-0.25890.03840.3688-0.07310.0130.38990.03460.4414-14.1874-22.51353.4602
164.0155-0.7854-0.56893.82851.49012.70590.1990.78660.0311-0.9647-0.0081-0.5745-0.70920.3156-0.25440.5759-0.06080.08290.5831-0.03030.4339-0.8996-25.0449-18.9475
171.2094-1.78790.80291.9185-0.23261.12540.10140.2432-0.182-0.0829-0.11490.138-0.01140.14890.01130.3879-0.07120.00660.38150.08140.4527-4.8099-23.976-10.4079
181.8318-0.42870.13541.17370.33373.0523-0.13230.0996-0.0657-0.0503-0.0071-0.1089-0.12440.14060.15860.3929-0.0264-0.02360.4155-0.00470.42176.0966-17.83424.4292
191.56220.8754-0.41850.401-0.09980.20350.0754-0.19830.0024-0.0631-0.13040.0951-0.0988-0.30810.04950.41660.0425-0.08130.49150.00510.43-21.60642.7211.5832
201.3867-0.4946-0.1153.48710.21010.740.21420.3920.088-0.7093-0.22430.3265-0.2717-0.35750.0210.59230.1006-0.1250.65150.07190.5187-30.111715.1383-20.8406
211.00430.32670.00441.7157-0.63441.61040.56420.48160.1773-0.385-0.16930.0769-0.4687-0.2361-0.4910.65260.22080.07350.63130.11590.7627-30.474124.3908-13.1099
221.43910.43340.3981.124-0.74451.2708-0.0346-0.04090.150.05120.08130.231-0.352-0.2653-0.03890.42980.08120.00070.45450.02540.5107-24.057214.2574-3.9174
234.42221.64341.71892.64221.56333.28780.15530.5146-0.2497-0.18510.0847-0.4517-0.38890.0496-0.27880.4778-0.02180.05350.56950.01370.4929-12.647711.7224-24.8608
240.5576-0.52840.771.2152-0.74022.8445-0.08690.22540.0480.04870.024-0.01270.04080.01840.07110.3912-0.0517-0.00210.4540.00570.4978-19.0787-6.8018-7.9526
250.808-0.5167-0.44621.1807-0.04590.8782-0.01290.0379-0.01470.0112-0.1389-0.31710.11930.24620.13550.47790.0315-0.05140.7390.02470.580564.52181.063345.6614
261.02451.0096-0.30141.38620.86921.27-0.3464-0.0326-0.6012-0.2187-0.0288-0.7550.82260.60510.39890.82160.21650.11940.75560.09480.836872.1815-16.475240.898
271.58150.18810.39241.2191-0.13620.5334-0.1173-0.16740.26710.0425-0.2046-0.73320.53890.43820.26730.55940.19980.00250.8380.08650.707670.6346-13.270755.7648
281.817-0.00610.00291.3177-0.5070.1132-0.2662-0.1650.2152-0.022-0.0907-0.3950.13170.32740.37950.36910.0225-0.09690.6063-0.01910.540761.0244-0.485550.8596
293.25820.9211-0.51472.22450.05981.6133-0.09850.5489-0.2067-0.24530.0456-0.15990.0981-0.02730.08860.58510.04860.06430.57210.02270.520253.4085-7.565531.0586
304.34760.378-0.58045.38110.55937.0419-0.6432-0.26910.246-1.0698-0.34840.1313-0.60341.16830.98480.38050.0276-0.0720.68010.04890.519865.458511.507136.1649
310.5413-0.2331-0.17461.61531.05643.2309-0.0710.2610.074-0.0733-0.0828-0.0808-0.08420.14510.17250.4275-0.0727-0.05320.5790.050.530955.988814.997343.7565
320.4686-1.2721-0.313.8824-1.40942.6455-0.1287-0.89440.6693-0.23790.2589-1.1375-0.06540.2136-0.09270.5416-0.0682-0.09320.7983-0.08480.737162.189914.972561.3712
331.07180.6308-0.44352.1584-1.26232.48550.13010.02040.2280.0298-0.0936-0.1439-0.35670.3507-0.00790.4758-0.0643-0.00240.4691-0.03530.47443.74539.879241.0483
342.89070.9359-0.89581.5094-0.72034.3873-0.23160.39180.4418-0.19310.5065-0.1174-0.84380.3419-0.1950.8255-0.2260.1120.71290.06480.756359.313844.439628.836
350.12810.11890.07133.0951-1.14950.5773-0.12920.07960.06550.35250.0932-0.6012-0.42920.40870.00610.5427-0.1811-0.09620.7221-0.04970.705365.306838.279340.9755
360.54820.2941-0.10591.7833-0.01530.27480.1082-0.04040.05190.2038-0.0946-0.2721-0.10570.16420.00040.4675-0.1445-0.05390.576-0.04880.537253.365132.307347.6942
374.7923-1.74170.69443.796-1.47451.45640.10930.41140.0862-0.7726-0.1168-0.27810.32150.312-0.00260.5985-0.02240.02660.57710.02120.441945.209725.900726.7144
381.98280.501-2.50271.5638-0.7473.5541-0.12240.2546-0.369-0.2055-0.034-0.09370.5329-0.54520.11380.5186-0.0396-0.0420.4748-0.01970.486933.313837.974943.8234
392.5653-0.551-0.52531.3535-0.67410.69630.02010.2108-0.0047-0.05570.1415-0.2508-0.0777-0.023-0.16440.54350.02710.00770.5234-0.03480.441333.249727.408649.8064
400.2724-0.02020.31481.1528-0.21231.2270.0744-0.2011-0.16010.3455-0.04880.09530.21-0.0254-0.0090.52610.00980.01860.45370.0490.46728.133-18.941261.8665
411.1306-0.155-0.13881.2685-0.15920.416-0.0484-0.3336-0.14990.3747-0.04660.05870.1746-0.00890.08980.6302-0.0180.00930.52290.06890.39827.6839-11.918367.383
420.51220.2369-0.45572.9332-0.33211.55820.01180.0508-0.06510.1420.0560.20150.1995-0.2098-0.08250.4903-0.0737-0.03490.47280.01760.456821.2204-13.350444.8898
432.5974-0.8532-0.49772.33530.38081.3862-0.1459-0.058-0.07620.27670.2184-0.03230.3250.1047-0.09590.53350.0184-0.00690.44290.01910.428445.2501-11.491652.8831
440.9514-0.127-0.21891.2712-0.38531.6574-0.1134-0.1976-0.04910.26620.0184-0.03420.06330.00770.08050.6010.0327-0.04750.5491-0.01530.34228.130514.766765.8872
452.6266-0.5003-1.60432.17220.50043.4574-0.24860.10950.07350.08190.04190.4888-0.2285-1.12790.2380.49460.0467-0.01480.7844-0.01310.59993.617925.624855.4774
463.2707-1.08590.70954.53491.17323.62620.0945-0.13060.9651-0.3016-0.46610.2062-0.7217-0.71760.29680.67470.19380.01840.6863-0.02260.61944.920537.223457.4739
474.1652-0.1191-0.70390.4923-0.62841.0335-0.34990.06830.30570.05170.25880.1709-0.2268-0.03320.04870.6191-0.0030.09020.4989-0.05710.517114.029838.229562.4283
481.107-0.9344-0.70991.54-0.37660.8570.02950.03230.1470.1783-0.0420.1242-0.1414-0.08030.0110.41280.0243-0.0060.4464-0.00480.343620.563324.475762.0558
493.93340.48961.0132.0529-0.34523.6637-0.39410.15410.1404-0.34590.09370.42720.0722-0.27110.27880.5048-0.0438-0.02830.7168-0.03970.490713.856821.488439.8758
503.015-0.81810.19852.59680.80461.10220.0317-0.19260.12570.4909-0.09650.26510.5002-0.09130.0350.5026-0.05640.05170.5220.0070.376618.94817.402764.1341
510.9962-0.9038-1.36723.19421.51161.97140.08020.2616-0.0079-0.3614-0.3580.06610.04720.11580.30940.7379-0.0283-0.01560.85760.04280.553921.9852-1.262747.0695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 242 )
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 389 )
5X-RAY DIFFRACTION5chain 'A' and (resid 390 through 446 )
6X-RAY DIFFRACTION6chain 'A' and (resid 447 through 486 )
7X-RAY DIFFRACTION7chain 'B' and (resid -2 through 90 )
8X-RAY DIFFRACTION8chain 'B' and (resid 91 through 368 )
9X-RAY DIFFRACTION9chain 'B' and (resid 369 through 445 )
10X-RAY DIFFRACTION10chain 'B' and (resid 446 through 486 )
11X-RAY DIFFRACTION11chain 'C' and (resid -5 through 18 )
12X-RAY DIFFRACTION12chain 'C' and (resid 19 through 56 )
13X-RAY DIFFRACTION13chain 'C' and (resid 57 through 242 )
14X-RAY DIFFRACTION14chain 'C' and (resid 243 through 270 )
15X-RAY DIFFRACTION15chain 'C' and (resid 271 through 363 )
16X-RAY DIFFRACTION16chain 'C' and (resid 364 through 389 )
17X-RAY DIFFRACTION17chain 'C' and (resid 390 through 445 )
18X-RAY DIFFRACTION18chain 'C' and (resid 446 through 486 )
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 39 )
20X-RAY DIFFRACTION20chain 'D' and (resid 40 through 232 )
21X-RAY DIFFRACTION21chain 'D' and (resid 233 through 257 )
22X-RAY DIFFRACTION22chain 'D' and (resid 258 through 368 )
23X-RAY DIFFRACTION23chain 'D' and (resid 369 through 427 )
24X-RAY DIFFRACTION24chain 'D' and (resid 428 through 486 )
25X-RAY DIFFRACTION25chain 'E' and (resid -2 through 77 )
26X-RAY DIFFRACTION26chain 'E' and (resid 78 through 257 )
27X-RAY DIFFRACTION27chain 'E' and (resid 258 through 292 )
28X-RAY DIFFRACTION28chain 'E' and (resid 293 through 363 )
29X-RAY DIFFRACTION29chain 'E' and (resid 364 through 427 )
30X-RAY DIFFRACTION30chain 'E' and (resid 428 through 445 )
31X-RAY DIFFRACTION31chain 'E' and (resid 446 through 486 )
32X-RAY DIFFRACTION32chain 'F' and (resid -5 through 12 )
33X-RAY DIFFRACTION33chain 'F' and (resid 13 through 77 )
34X-RAY DIFFRACTION34chain 'F' and (resid 78 through 242 )
35X-RAY DIFFRACTION35chain 'F' and (resid 243 through 270 )
36X-RAY DIFFRACTION36chain 'F' and (resid 271 through 363 )
37X-RAY DIFFRACTION37chain 'F' and (resid 364 through 427 )
38X-RAY DIFFRACTION38chain 'F' and (resid 428 through 446 )
39X-RAY DIFFRACTION39chain 'F' and (resid 447 through 486 )
40X-RAY DIFFRACTION40chain 'G' and (resid -1 through 242 )
41X-RAY DIFFRACTION41chain 'G' and (resid 243 through 368 )
42X-RAY DIFFRACTION42chain 'G' and (resid 369 through 427 )
43X-RAY DIFFRACTION43chain 'G' and (resid 428 through 486 )
44X-RAY DIFFRACTION44chain 'H' and (resid -2 through 33 )
45X-RAY DIFFRACTION45chain 'H' and (resid 34 through 91 )
46X-RAY DIFFRACTION46chain 'H' and (resid 92 through 242 )
47X-RAY DIFFRACTION47chain 'H' and (resid 243 through 270 )
48X-RAY DIFFRACTION48chain 'H' and (resid 271 through 368 )
49X-RAY DIFFRACTION49chain 'H' and (resid 369 through 427 )
50X-RAY DIFFRACTION50chain 'H' and (resid 428 through 470 )
51X-RAY DIFFRACTION51chain 'H' and (resid 471 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