[English] 日本語
Yorodumi
- PDB-7kzd: Crystal structure of KabA from Bacillus cereus UW85 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kzd
TitleCrystal structure of KabA from Bacillus cereus UW85 in complex with the reduced internal aldimine and with bound Glutarate
ComponentsAminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / Kanosamine / Biosynthesis / Aminotransferase / KabA
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
GLUTARIC ACID / Chem-PLR / Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPrasertanan, T. / Palmer, D.R.J. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Snapshots along the catalytic path of KabA, a PLP-dependent aminotransferase required for kanosamine biosynthesis in Bacillus cereus UW85.
Authors: Prasertanan, T. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
E: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
F: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
G: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
H: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,12066
Polymers407,8718
Non-polymers5,24958
Water29,3101627
1
A: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The data suggest that KabA is of high purity and is a tetramer in solution using size exclusion chromatography to estimate molecular weight corresponded to the observed ...Evidence: gel filtration, The data suggest that KabA is of high purity and is a tetramer in solution using size exclusion chromatography to estimate molecular weight corresponded to the observed molecular weight based on Native (non-denaturing) gel electrophoresis analysis
  • 103 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)103,31117
Polymers101,9682
Non-polymers1,34315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-10 kcal/mol
Surface area34170 Å2
MethodPISA
2
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,55921
Polymers101,9682
Non-polymers1,59219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint5 kcal/mol
Surface area34420 Å2
MethodPISA
3
E: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
H: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,12514
Polymers101,9682
Non-polymers1,15712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-3 kcal/mol
Surface area34670 Å2
MethodPISA
4
F: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
G: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,12514
Polymers101,9682
Non-polymers1,15712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-7 kcal/mol
Surface area34760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.940, 93.580, 106.890
Angle α, β, γ (deg.)108.840, 92.330, 90.080
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme / KabA


Mass: 50983.910 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: kabA, GE376_30835 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C0JRF5, aspartate transaminase
#2: Chemical
ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H12NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GUA / GLUTARIC ACID / Glutaric acid


Mass: 132.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1627 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, Sodium Chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.814 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.814 Å / Relative weight: 1
ReflectionResolution: 1.9→48.413 Å / Num. obs: 257845 / % possible obs: 95.92 % / Redundancy: 2.1 % / CC1/2: 0.994 / Rrim(I) all: 0.091 / Net I/σ(I): 6.86
Reflection shellResolution: 1.9→1.968 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 25515 / CC1/2: 0.716 / Rrim(I) all: 0.641 / % possible all: 95.28

-
Processing

Software
NameVersionClassification
PHENIXdev_2398refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
AutoProcessdata reduction
AutoProcessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KZ3
Resolution: 1.9→48.413 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 12881 5 %
Rwork0.2071 244573 -
obs0.2092 257454 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.02 Å2 / Biso mean: 39.4364 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 1.9→48.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28358 0 220 1639 30217
Biso mean--59.66 39.15 -
Num. residues----3504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729121
X-RAY DIFFRACTIONf_angle_d0.89839188
X-RAY DIFFRACTIONf_chiral_restr0.0534404
X-RAY DIFFRACTIONf_plane_restr0.0055004
X-RAY DIFFRACTIONf_dihedral_angle_d16.30917876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.35144190.3015798695
1.9216-1.94420.31524300.2798817195
1.9442-1.96790.31734250.2687807896
1.9679-1.99280.31434310.2751817496
1.9928-2.0190.3024280.2595815996
2.019-2.04670.3074270.2539810096
2.0467-2.07590.29024270.2466812095
2.0759-2.10690.28494270.2431811696
2.1069-2.13990.29424310.2356818196
2.1399-2.17490.27174290.228816296
2.1749-2.21240.28734290.2296813996
2.2124-2.25270.28094280.2245812796
2.2527-2.2960.26754330.2186822896
2.296-2.34290.28034300.2258816896
2.3429-2.39380.28074290.2241815896
2.3938-2.44950.26994290.2171815396
2.4495-2.51070.26734280.2227814096
2.5107-2.57860.26694300.2156817696
2.5786-2.65450.26164300.2141815796
2.6545-2.74020.26014310.2131819296
2.7402-2.83810.2674310.2144817696
2.8381-2.95170.25664330.2151822897
2.9517-3.0860.25814310.2123819196
3.086-3.24870.24344320.2042820096
3.2487-3.45220.21794300.1908817896
3.4522-3.71860.2324270.187810496
3.7186-4.09270.20294300.1732817996
4.0927-4.68450.19474320.1671819496
4.6845-5.90030.2264320.1889821097
5.9003-48.4130.24324320.2047802895
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)
13.9013-0.0472-0.86423.38420.01513.7836-0.0207-0.4169-0.41980.34950.02020.4457-0.0761-0.7011-0.00450.2672-0.01910.05760.43390.03860.3985-12.5569-5.134117.4492
22.0045-0.17710.26770.8547-0.01071.4796-0.0626-0.0457-0.10180.0243-0.07540.04380.0611-0.01140.08860.22520.02090.01680.16830.00760.28018.6836-0.19275.78
30.8610.01980.09973.52630.59683.50870.11380.4194-0.4149-0.4639-0.15690.24650.283-0.08020.04110.34080.0243-0.04510.2854-0.10140.38051.4931-5.4029-15.1403
42.8163-0.3739-0.37721.52350.51952.51290.01010.0359-0.39750.0154-0.0298-0.06120.20670.16280.0030.23420.01670.00490.1370.02190.265713.9447-7.3655-0.334
52.1986-0.68110.34581.3306-0.09031.36360.06050.24710.1067-0.2128-0.15360.237-0.1408-0.22570.01190.26250.041-0.03510.2251-0.01610.2774-7.818410.5841-2.6715
64.50970.1939-0.25721.85650.05573.63180.0576-0.3122-0.22370.184-0.05290.4390.0029-0.45680.01210.2472-0.05330.01730.29490.06080.369934.304440.337317.4491
71.56170.06490.50720.7056-0.30791.13660.00490.0246-0.0139-0.0442-0.07430.1162-0.0952-0.1262-0.00910.20950.04310.00110.1480.00910.195555.440246.45865.8203
82.3148-1.0863-0.16253.9424-0.03334.0245-0.0170.2726-0.1687-0.3596-0.11650.3855-0.0523-0.30550.05170.31050.0976-0.06970.3645-0.0460.23849.260247.6867-14.835
92.0779-0.76710.05641.1729-0.00820.97570.15340.376-0.0568-0.2181-0.15480.1926-0.0722-0.1411-0.00640.25130.027-0.04440.2383-0.0060.267346.166648.5572-4.069
103.82681.1199-2.47622.67030.41044.776-0.3028-0.0643-0.12260.10710.0881-0.6762-0.3080.48420.18220.3135-0.1101-0.05590.3325-0.01210.609145.16218.869719.4823
111.96150.09070.70670.88130.16751.6334-0.0349-0.10410.02530.01570.0558-0.1616-0.11620.37030.02340.2701-0.0079-0.01490.32420.00650.309531.30339.007612.4997
121.4877-0.15810.26691.92040.63260.9319-0.04440.5104-0.0264-0.36020.086-0.3669-0.17010.75910.04350.3398-0.07820.06260.7041-0.02730.398439.54836.9462-5.4433
134.60662.11192.36213.20950.0013.9977-0.13260.49840.3904-0.3640.08060.1702-0.487-0.07910.07670.3870.04530.01190.30850.05110.329418.582414.6153-6.7242
140.025-0.03110.1481.81740.24461.76050.06840.1994-0.26790.04440.0405-0.65490.0990.90950.4040.19890.0954-0.09110.5663-0.05930.535846.3175-1.271513.1674
153.37320.03291.43262.04040.05681.70930.17190.936-0.6447-0.4008-0.1176-0.23530.09540.1389-0.31540.48280.2467-0.04110.7618-0.26390.686539.042-11.458-5.1844
161.726-0.944-0.07181.88910.44482.4243-0.03060.3435-0.4564-0.021-0.0402-0.27730.1660.46380.18670.22680.092-0.05470.51380.00920.550248.1414-7.697913.3092
179.3365.78695.50495.39661.07716.9342-0.78630.5529-0.1885-0.87730.34870.0551-0.587-0.46580.34621.12190.32890.07371.5573-0.12050.43432.3094-2.47357.1273
182.70150.60190.63073.2756-0.18383.1548-0.1231-0.21370.59310.5990.035-0.4492-0.52850.4860.04170.4234-0.0597-0.04030.3971-0.0990.498991.040265.594423.1513
190.96210.7719-0.46061.45420.28220.6960.0729-0.15470.14530.0945-0.0871-0.01530.02290.12540.0490.23890.0423-0.0190.2721-0.02840.160872.570954.919317.494
201.0507-0.35360.30191.3440.10221.46320.07030.55450.0479-0.2195-0.0004-0.2697-0.17470.5616-0.05220.266-0.05460.02870.50970.01870.241783.557555.4291-5.8005
214.53672.63221.7952.5438-0.56864.7178-0.07660.35720.3528-0.2510.21490.4112-0.3515-0.4302-0.15090.32140.05630.01140.30720.04880.307264.586461.8251-6.5865
223.3463-1.1055-0.22361.86090.35530.9380.05040.3564-0.06480.0317-0.0436-0.30020.03450.2629-0.02730.1928-0.0003-0.03220.2902-0.03540.269593.163647.399713.0941
234.39890.19590.93812.8687-0.70560.3984-0.06851.1596-0.4612-0.42480.1556-0.01670.09650.4185-0.18860.28390.0886-0.08690.5693-0.17170.552188.386937.2664-5.1253
243.2166-0.94630.13262.33120.93086.08390.1216-0.0528-0.370.0816-0.1684-0.00790.1833-0.1014-0.06540.1409-0.0349-0.05160.25730.03130.267894.873141.610618.4653
2520.50092.00010.02220.44598.9340.05040.3459-0.1838-0.2026-0.0124-0.12290.28310.07490.01340.94350.16720.21960.757-0.34540.63979.435545.52657.1021
264.1733-0.5738-0.99682.64240.68233.55760.15950.5471-0.5717-0.2204-0.1535-0.57270.22590.68350.04610.26820.04850.03620.42770.03340.4389-11.9412-20.1714-59.781
271.19910.23430.26460.6719-0.06031.0040.01220.0555-0.0381-0.0104-0.1049-0.0856-0.06740.02730.10030.2994-0.03680.02250.1991-0.01680.2965-28.3414-12.2862-52.3258
280.326-0.78190.19862.6459-0.27952.90540.0238-0.5318-0.44720.4056-0.2709-0.19640.3130.24060.13110.3446-0.0969-0.04650.31460.10220.2712-22.892-16.1998-28.8668
290.62850.4249-0.27791.08640.09451.48970.0381-0.0571-0.24210.1404-0.0781-0.07090.2690.01240.00370.2608-0.04670.01920.14120.00630.2067-34.6874-20.906-41.7019
301.43590.61920.57181.75660.6611.79520.0706-0.15910.10710.3109-0.1533-0.2245-0.01810.1899-0.010.2688-0.0737-0.0280.22980.03740.2936-15.8382-1.8871-42.0945
312.9571-1.63411.19151.31810.17983.37280.20770.2629-0.7177-0.1589-0.0686-0.2604-0.07850.1456-0.13260.21470.02230.00490.270.0040.568233.69925.4972-59.9854
322.246-0.06020.50880.0587-0.36591.19250.05910.4206-0.0923-0.0532-0.1003-0.3319-0.15130.24770.03630.3138-0.00340.03480.34740.0210.379526.120840.3593-63.8733
331.4640.7850.58030.92820.31582.08180.05-0.2419-0.22590.0912-0.18840.01750.0704-0.03210.14590.2832-0.0403-0.0110.19680.0380.351110.323928.6811-42.4246
340.0393-0.11920.04081.2009-0.24692.74870.1653-0.4619-0.62930.3311-0.3147-0.39420.23740.26130.22550.3781-0.0933-0.10250.42510.18130.445523.31230.1474-29.0944
350.62150.4985-0.71690.5285-0.20661.11240.0479-0.1209-0.43030.0748-0.1627-0.23980.1020.01960.00080.2287-0.0392-0.04510.17850.06870.342311.077425.6371-41.7823
362.060.880.67511.33030.29321.21280.1794-0.4357-0.03970.2981-0.1856-0.3044-0.04750.1474-0.00570.2582-0.0744-0.06090.26180.03820.351530.085643.026-43.2993
372.14230.39180.59762.26410.91671.74930.2739-0.47580.04040.2802-0.1379-0.386-0.10240.282-0.22740.2826-0.1275-0.07870.31660.08440.387932.598846.5589-40.3653
382.1439-1.3253-0.37763.20490.29842.7131-0.07250.35570.5606-0.62530.00270.389-0.3286-0.3710.04160.32350.0427-0.06320.29960.08710.4366-22.028853.2212-67.723
391.6185-0.15210.03760.6449-0.39731.19510.0185-0.06820.07680.0735-0.0306-0.0724-0.076-0.12770.00180.2206-0.0009-0.01790.1905-0.04680.2294-5.279441.9602-51.1962
400.58190.45440.15171.167-0.49962.2913-0.0383-0.38290.1020.22140.00840.1476-0.1985-0.55640.00910.2620.0533-0.00410.4753-0.07880.2316-17.493742.9737-39.6481
411.993-1.19451.71522.39630.18195.38150.0752-0.19820.36110.2462-0.0942-0.409-0.28120.3252-0.0340.2894-0.0896-0.0240.2813-0.050.36544.505349.2142-37.9023
421.45550.32790.34741.6242-0.06330.8030.1021-0.2244-0.14720.0935-0.0490.1890.0686-0.1999-0.09610.1853-0.0099-0.00870.28010.01340.2254-23.009131.0871-54.2453
439.4678-2.9223-4.37145.35084.06393.6747-1.73910.22910.61291.51820.6626-1.5152-0.27290.06221.10091.3936-0.04210.19830.52360.30921.1459-8.210932.4429-51.0951
440.6872-0.505-0.78155.5574-1.38782.0251-0.15720.00060.3684-0.08110.08970.3999-0.7683-0.73020.02230.35050.1472-0.05330.5376-0.03520.6288-68.87046.5558-64.2333
451.4337-0.05480.30790.9440.06791.25820.02020.0010.18770.0021-0.05680.182-0.1593-0.36850.03990.27740.02660.01420.2497-0.03220.3126-55.1092-4.8922-54.2812
461.0008-0.1434-0.79471.4414-0.48832.38930.0096-0.32060.06410.32090.02940.2921-0.2419-0.6419-0.0870.35650.02740.08420.584-0.10290.382-64.3592-4.5467-40.2821
472.1409-0.81531.05051.48260.2743.8607-0.0232-0.14730.56090.4169-0.0783-0.0989-0.22250.1850.12570.4283-0.06670.02850.2868-0.07050.3841-42.38162.0026-37.7071
480.59070.04160.6262.2549-0.09071.66880.0197-0.1422-0.0102-0.0441-00.64330.1637-0.6220.04240.2306-0.0363-0.00610.4005-0.02690.4223-69.9127-13.8679-58.0901
491.4350.19981.05662.044-0.04810.85410.1852-0.3612-0.20550.2011-0.08770.28450.4938-0.428600.3009-0.13460.02660.57740.01160.431-67.5018-22.022-49.9038
502-3.03729.10940.6234-1.86975.6080.0496-0.0405-0.04470.2892-0.0714-0.19510.153-0.1155-0.00171.5035-0.09270.19510.74960.48910.9456-55.3528-14.9009-51.3347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 67 )A6 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 158 )A68 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 229 )A159 - 229
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 303 and resid 501)A230 - 303
5X-RAY DIFFRACTION5chain 'A' and (resid 304 through 443 )A304 - 443
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 67 )B5 - 67
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 158 )B68 - 158
8X-RAY DIFFRACTION8chain 'B' and (resid 159 through 185 )B159 - 185
9X-RAY DIFFRACTION9chain 'B' and (resid 186 through 443 and resid 501)B186 - 443
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 47 )C6 - 47
11X-RAY DIFFRACTION11chain 'C' and (resid 48 through 158 )C48 - 158
12X-RAY DIFFRACTION12chain 'C' and (resid 159 through 262 and resid 502)C159 - 262
13X-RAY DIFFRACTION13chain 'C' and (resid 263 through 303 )C263 - 303
14X-RAY DIFFRACTION14chain 'C' and (resid 304 through 378 )C304 - 378
15X-RAY DIFFRACTION15chain 'C' and (resid 379 through 407 )C379 - 407
16X-RAY DIFFRACTION16chain 'C' and (resid 408 through 443 )C408 - 443
17X-RAY DIFFRACTION17chain 'C' and (resid 501 through 501 )C502
18X-RAY DIFFRACTION18chain 'D' and (resid 6 through 67 )D6 - 67
19X-RAY DIFFRACTION19chain 'D' and (resid 68 through 121 )D68 - 121
20X-RAY DIFFRACTION20chain 'D' and (resid 122 through 262 and resid 502)D122 - 262
21X-RAY DIFFRACTION21chain 'D' and (resid 263 through 303 )D263 - 303
22X-RAY DIFFRACTION22chain 'D' and (resid 304 through 378 )D304 - 378
23X-RAY DIFFRACTION23chain 'D' and (resid 379 through 415 )D379 - 415
24X-RAY DIFFRACTION24chain 'D' and (resid 416 through 443 )D416 - 443
25X-RAY DIFFRACTION25chain 'D' and (resid 501 through 501 )D502
26X-RAY DIFFRACTION26chain 'E' and (resid 7 through 47 )E7 - 47
27X-RAY DIFFRACTION27chain 'E' and (resid 48 through 168 )E48 - 168
28X-RAY DIFFRACTION28chain 'E' and (resid 169 through 211 )E169 - 211
29X-RAY DIFFRACTION29chain 'E' and (resid 212 through 303 and resid 501)E212 - 303
30X-RAY DIFFRACTION30chain 'E' and (resid 304 through 443 )E304 - 443
31X-RAY DIFFRACTION31chain 'F' and (resid 7 through 47 )F7 - 47
32X-RAY DIFFRACTION32chain 'F' and (resid 48 through 101 )F48 - 101
33X-RAY DIFFRACTION33chain 'F' and (resid 102 through 168 )F102 - 168
34X-RAY DIFFRACTION34chain 'F' and (resid 169 through 211 )F169 - 211
35X-RAY DIFFRACTION35chain 'F' and (resid 212 through 303 and resid 501)F212 - 303
36X-RAY DIFFRACTION36chain 'F' and (resid 304 through 401 )F304 - 401
37X-RAY DIFFRACTION37chain 'F' and (resid 402 through 443 )F402 - 443
38X-RAY DIFFRACTION38chain 'G' and (resid 5 through 67 )G5 - 67
39X-RAY DIFFRACTION39chain 'G' and (resid 68 through 168 )G68 - 168
40X-RAY DIFFRACTION40chain 'G' and (resid 169 through 262 and resid 501)G169 - 262
41X-RAY DIFFRACTION41chain 'G' and (resid 263 through 303 )G263 - 303
42X-RAY DIFFRACTION42chain 'G' and (resid 304 through 443 )G304 - 443
43X-RAY DIFFRACTION43chain 'F' and (resid 502 through 502 )F502
44X-RAY DIFFRACTION44chain 'H' and (resid 6 through 47 )H6 - 47
45X-RAY DIFFRACTION45chain 'H' and (resid 48 through 175 )H48 - 175
46X-RAY DIFFRACTION46chain 'H' and (resid 176 through 262 and resid 501)H176 - 262
47X-RAY DIFFRACTION47chain 'H' and (resid 263 through 303 )H263 - 303
48X-RAY DIFFRACTION48chain 'H' and (resid 304 through 378 )H304 - 378
49X-RAY DIFFRACTION49chain 'H' and (resid 379 through 443 )H379 - 443
50X-RAY DIFFRACTION50chain 'E' and (resid 502 through 502 )E502

+
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