[English] 日本語
Yorodumi
- PDB-6mn5: Crystal structure of aminoglycoside acetyltransferase AAC(3)-IVa,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mn5
TitleCrystal structure of aminoglycoside acetyltransferase AAC(3)-IVa, H154A mutant, in complex with gentamicin C1A
ComponentsAminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
KeywordsTRANSFERASE/ANTIBIOTIC / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / COENZYME A / GENTAMICIN / AAC(3)-IVA / CSGID / TRANSFERASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / National Institute of Allergy and Infectious Diseases / NIAID / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / response to antibiotic / metal ion binding
Similarity search - Function
Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like
Similarity search - Domain/homology
Chem-LLL / Chem-PE3 / Aminoglycoside N(3)-acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsStogios, P.J. / Evdokimova, E. / Kim, Y. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 6, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
B: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
C: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
D: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
E: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
F: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,75779
Polymers169,8986
Non-polymers10,85973
Water9,170509
1
A: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,08317
Polymers28,3161
Non-polymers1,76616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,53115
Polymers28,3161
Non-polymers2,21514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,59316
Polymers28,3161
Non-polymers2,27715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,62316
Polymers28,3161
Non-polymers2,30715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5569
Polymers28,3161
Non-polymers1,2408
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3706
Polymers28,3161
Non-polymers1,0545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.609, 131.881, 266.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa


Mass: 28316.393 Da / Num. of mol.: 6 / Mutation: H154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: aacC4, aac(3), aac(3)-IV, aac(3)IV, aac3-VI, aac3-VI_1, aac3-VI_2, B9T59_28975, BEN53_26235, BJJ90_27515, BK373_27930, BK400_28640, BVL39_27730, BZL31_07055, BZL69_29365, C5P01_27985, C7235_ ...Gene: aacC4, aac(3), aac(3)-IV, aac(3)IV, aac3-VI, aac3-VI_1, aac3-VI_2, B9T59_28975, BEN53_26235, BJJ90_27515, BK373_27930, BK400_28640, BVL39_27730, BZL31_07055, BZL69_29365, C5P01_27985, C7235_00480, CR538_26885, CWS33_26775, CXB56_01995, pEC012_00026, SAMEA3472055_02859, SAMEA3472064_03809, SAMEA3472078_05206, SAMEA3472108_05065, SAMEA3472117_05674, SAMEA3472119_04576, SAMEA3472121_05663, SAMEA3485115_04534, SAMEA3751392_04817, SAMEA3752267_04833, SAMEA3752372_05888, SAMEA3752378_04585, SAMEA3752509_02517, SAMEA3752558_04925, SAMEA3752685_02521, SAMEA3753064_04967, SAMEA3753137_02787, SAMEA3753290_03667, SAMEA3753300_05389, SAMEA3753355_02348
Plasmid: pET19bTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold
References: UniProt: Q306W4, aminoglycoside 3-N-acetyltransferase

-
Non-polymers , 7 types, 582 molecules

#2: Chemical
ChemComp-LLL / (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL / GENTAMICIN C1A


Mass: 449.542 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H39N5O7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H58O15
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7, 30% PEG 1k, 1 mM gentamicin

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.58→40 Å / Num. obs: 83508 / % possible obs: 95.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.048 / Net I/σ(I): 14.08
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 1.08 / Num. unique all: 3527 / CC1/2: 0.703 / Rpim(I) all: 0.371 / % possible all: 82

-
Processing

Software
NameVersionClassification
PHENIX(dev_3026: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMA

3sma


Resolution: 2.58→38.401 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 2000 2.4 %RANDOM
Rwork0.1866 ---
obs0.1874 83420 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.58→38.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11813 0 608 509 12930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612697
X-RAY DIFFRACTIONf_angle_d0.87917239
X-RAY DIFFRACTIONf_dihedral_angle_d22.294849
X-RAY DIFFRACTIONf_chiral_restr0.0441922
X-RAY DIFFRACTIONf_plane_restr0.0052206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5786-2.6430.28121230.26815014X-RAY DIFFRACTION83
2.643-2.71450.29261350.2585496X-RAY DIFFRACTION93
2.7145-2.79430.31291430.25535801X-RAY DIFFRACTION96
2.7943-2.88450.27891430.24495828X-RAY DIFFRACTION97
2.8845-2.98750.26331440.24955885X-RAY DIFFRACTION97
2.9875-3.10710.28011450.22855924X-RAY DIFFRACTION99
3.1071-3.24850.25791470.21715962X-RAY DIFFRACTION99
3.2485-3.41960.25451450.20775917X-RAY DIFFRACTION98
3.4196-3.63370.20491440.19065846X-RAY DIFFRACTION97
3.6337-3.9140.19451470.16526008X-RAY DIFFRACTION98
3.914-4.30740.18071470.15055949X-RAY DIFFRACTION98
4.3074-4.92960.19491430.14855845X-RAY DIFFRACTION96
4.9296-6.20660.22471480.17835985X-RAY DIFFRACTION97
6.2066-38.40490.2081460.18055960X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.89163.9432-4.34433.9223-4.35124.69720.1701-0.67630.1760.55410.15620.26860.0766-1.0248-0.38540.4419-0.05070.01280.6719-0.04050.433727.26128.24826.8004
27.5337-0.7592-3.65786.4857-1.92358.85160.24540.0634-0.10240.2675-0.16040.30850.0005-0.5196-0.14320.2069-0.0417-0.04780.44060.00930.299628.860825.41216.908
32.6647-0.4058-0.14032.86250.89232.34250.20460.4206-0.2545-0.2022-0.1568-0.03850.1172-0.4055-0.02040.2939-0.0329-0.00150.6751-0.03950.410627.621816.47954.0604
48.858-0.7509-0.80654.25295.40236.86530.09331.9744-0.4678-1.2103-0.0062-0.37060.06390.285-0.16230.5044-0.030.0890.7793-0.03060.491136.939520.8487-1.4933
57.8521-2.45560.54943.971-1.04476.35440.16710.428-0.1045-0.0886-0.16-0.7113-0.06330.7401-0.00150.2404-0.05140.01230.4605-0.09840.462242.915519.72728.798
64.68633.09066.53766.50453.79319.11210.210.6378-0.955-0.2058-0.1234-0.1690.0991-0.0311-0.12710.6284-0.01910.10850.7835-0.11250.751541.85065.0038-2.1002
78.92834.21166.88093.78092.81862.08470.2761.0718-0.516-0.5226-0.14210.1574-0.0511-0.0855-0.0550.71210.04590.0290.847-0.27770.730238.04824.1063-2.5632
85.4966-4.5133-2.05415.82042.75882.38840.0306-0.2576-0.09470.38450.0235-0.4970.1810.278-0.04430.333-0.0068-0.07730.45590.03460.473349.037313.013215.9366
95.1691-1.3351-0.29163.180.82096.09550.09780.64440.1248-0.36740.0953-0.1239-0.20620.747-0.16940.3402-0.0642-0.08090.6276-0.04940.42056.818320.8858-5.8845
106.7575-2.27973.48912.8637-2.00344.44470.0267-0.0017-0.3277-0.09850.0996-0.04930.02610.2046-0.12290.2925-0.0423-0.00360.4291-0.03990.343710.97115.61310.7479
116.86950.76563.12318.143-4.22744.08760.6462-1.4058-0.42450.9841-0.23480.97390.0762-0.9019-0.57120.4992-0.03240.05860.82310.03590.60271.331914.414818.4511
123.77892.93561.43674.16580.01515.73420.234-0.3675-0.25640.06890.12940.41060.2335-0.1976-0.29320.28450.0086-0.05760.50920.02530.546-3.934710.7358.454
137.7505-1.30295.29862.587-4.10068.0716-0.023-0.1927-0.50.11740.3687-0.1650.12990.0646-0.58440.5737-0.0235-0.1380.58240.08650.79072.4184-1.851120.2415
143.3867-0.63043.64640.93740.33286.04420.0895-0.3792-0.80240.5264-0.415-0.42670.08220.85230.50230.8071-0.1832-0.17440.86960.34170.9976.3397-1.454620.524
154.40671.4539-2.52918.1293-6.25415.6021-0.04850.3956-0.2812-0.85530.39681.16840.3601-0.4017-0.27080.5094-0.0575-0.17420.6049-0.12930.5445-7.37647.9509-3.9954
164.18151.1856-0.43866.6003-2.71454.20220.14520.2869-1.30320.04930.0312-0.08720.7706-0.002-0.16750.4519-0.0241-0.15970.5226-0.12030.8192-7.5405-1.5065.1951
173.9421-1.6152.5959.4040.77392.532-0.03-0.59390.01750.52890.5010.1614-0.1418-0.0642-0.53050.4053-0.02750.07060.6549-0.0870.37161.183318.0082-18.013
181.6450.7823-1.38539.4234-4.56577.1246-0.1793-0.0144-0.0997-0.06150.3548-0.25020.2957-0.1104-0.14830.4007-0.0673-0.03580.6086-0.1320.41983.31617.5728-28.1102
194.4607-0.81022.13347.7602-0.61064.5477-0.14220.0657-0.30050.28440.177-0.78870.43910.8892-0.0580.4512-0.05630.09620.6132-0.06820.38510.59210.3823-41.2472
203.8871-0.4142-0.65996.85251.44044.83150.03860.5890.1008-0.74420.2164-0.4947-0.19170.3637-0.22260.5102-0.04650.0430.5423-0.0550.36047.545815.9484-44.316
219.32521.63140.52244.07280.25922.73860.24970.24250.4665-0.3755-0.0105-0.5987-0.48720.9315-0.14980.4709-0.07380.14360.6269-0.07880.462214.651925.574-38.0757
222.74073.73661.24436.95231.1930.792-0.23030.4051-0.3136-0.69220.8481-0.7582-0.24930.7537-0.62340.71590.05060.19341.1508-0.24950.764324.341713.6564-49.6684
237.15033.6093-6.68646.5442-4.65839.2090.4526-0.56170.70870.40630.0569-0.5205-0.78291.0007-0.4550.4988-0.10420.0350.7953-0.16640.596617.801930.0571-29.3212
247.0202-0.1774-3.31952.2179-0.90147.8545-0.8656-0.3428-0.0146-0.15211.1266-1.0980.00241.8754-0.32260.6697-0.13860.09361.3178-0.27671.124735.486523.1663-37.2566
258.3083-4.7573-5.33224.14565.00346.14850.530.27420.359-0.3367-0.068-0.72790.16860.1728-0.41250.51970.0166-0.03680.59160.05250.377634.766826.034535.0156
263.1034-1.24290.49644.3893-2.92328.6422-0.1366-0.1287-0.44280.5340.35910.40890.0364-0.3794-0.17980.41190.00410.05540.54770.04620.35629.262320.516652.8729
273.57682.1431-4.73175.9809-4.58156.9557-0.4624-1.23110.29381.25820.85450.8746-0.7731-0.8417-0.31771.08980.40570.17541.11580.11370.695922.872426.639463.3881
287.05992.20355.42218.8916-2.58026.5144-0.479-1.16410.42261.33160.33130.4269-0.9458-1.360.15880.65960.220.17570.75530.07310.669321.497532.293854.6899
297.1556-2.5484-1.1383.13980.34360.2170.08520.332-0.1741.04870.59570.5012-0.3699-1.8724-0.58830.74610.13160.20721.09640.27110.843211.246321.675858.2083
306.0726-6.63375.97647.2693-6.53675.9574-0.1536-1.0872-0.0808-0.57320.1976-0.22370.9353-0.2165-0.17381.11330.04990.49441.41760.39761.295311.918913.993364.9217
318.9093-0.9093-4.13624.80151.27455.86580.07380.00920.42290.18480.0980.9612-0.3426-1.2196-0.1820.570.18170.070.94640.15980.602213.262132.28144.0248
323.498-3.24943.5537.5443-0.97874.9412-0.08531.1535-0.11680.21121.09021.27760.5296-1.7846-0.98080.6619-0.1350.09411.65760.44931.355-1.454218.75450.889
334.463-1.7608-4.22388.3288-0.41984.5040.347-0.04230.56940.7214-0.8942-1.0534-1.56481.55440.7360.8622-0.1559-0.14231.13140.40810.834447.66211.003972.4506
342.8946-2.07860.2414.4824-4.9447.84680.09670.467-0.0731-1.2944-0.9645-0.38361.86051.30910.31141.11610.20970.26110.80180.25910.571843.01424.997752.1118
351.7433-0.1378-1.99460.01430.15212.3157-0.164-0.5372-1.9421-1.1766-0.5375-0.78472.0532.53930.77661.89021.13920.5511.50170.30931.184952.7587-2.385652.4346
360.3195-0.0952-0.96533.3741-1.10922.2661-0.26210.3867-0.546-1.207-0.28530.14122.70440.7090.40332.61870.54020.30331.18340.20180.965144.8861-10.672754.3533
373.791.34381.05068.63674.11111.9642-0.7397-0.4168-0.18040.4045-0.7321-0.3330.8191-0.2825-0.30473.6193-0.3060.00270.28880.64881.70636.6706-23.601456.0957
385.62290.9075-0.49666.31962.22718.554-0.42090.15320.25680.5788-1.10241.06141.303-2.74170.95250.9294-0.19340.17651.251-0.51150.7032-8.1828-3.2588-46.9516
393.98371.38421.43727.26980.66688.46410.6964-0.5512-0.82631.7906-0.6379-0.08683.3285-1.0624-0.03611.8159-0.1772-0.02020.8323-0.08350.60050.9965-6.2277-28.9493
402.3767-0.71130.33860.3363-0.32180.4231-0.2938-1.4204-2.1221.9163-0.18320.18752.2337-1.54920.7462.6591-0.84830.26021.40140.27781.2642-8.0751-15.8554-32.6529
41-0.1008-0.14760.14660.4898-0.21760.00140.5458-0.4541-0.56650.7468-0.3258-0.73713.24440.1962-0.20173.44390.1971-0.33071.06830.00551.21198.7642-18.1059-26.9253
423.27691.94820.81717.18960.27890.89020.4848-0.1928-1.20521.2874-0.55540.04083.1365-0.3678-0.02022.8983-0.35070.09321.1386-0.23131.0189-4.1056-23.0476-42.5376
435.2559-3.8767-1.83434.1847-1.54166.7469-0.9333-0.269-0.91032.42610.5013-0.76423.38030.75220.68943.60560.743-0.40911.3742-0.43142.163712.3791-31.3087-37.6657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 159 )
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 190 )
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 257 )
9X-RAY DIFFRACTION9chain 'B' and (resid -1 through 39 )
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 103 )
11X-RAY DIFFRACTION11chain 'B' and (resid 104 through 128 )
12X-RAY DIFFRACTION12chain 'B' and (resid 129 through 159 )
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 174 )
14X-RAY DIFFRACTION14chain 'B' and (resid 175 through 190 )
15X-RAY DIFFRACTION15chain 'B' and (resid 191 through 213 )
16X-RAY DIFFRACTION16chain 'B' and (resid 214 through 257 )
17X-RAY DIFFRACTION17chain 'C' and (resid -1 through 17 )
18X-RAY DIFFRACTION18chain 'C' and (resid 18 through 52 )
19X-RAY DIFFRACTION19chain 'C' and (resid 53 through 83 )
20X-RAY DIFFRACTION20chain 'C' and (resid 84 through 128 )
21X-RAY DIFFRACTION21chain 'C' and (resid 129 through 159 )
22X-RAY DIFFRACTION22chain 'C' and (resid 160 through 190 )
23X-RAY DIFFRACTION23chain 'C' and (resid 191 through 232 )
24X-RAY DIFFRACTION24chain 'C' and (resid 233 through 257 )
25X-RAY DIFFRACTION25chain 'D' and (resid -1 through 17 )
26X-RAY DIFFRACTION26chain 'D' and (resid 18 through 103 )
27X-RAY DIFFRACTION27chain 'D' and (resid 104 through 128 )
28X-RAY DIFFRACTION28chain 'D' and (resid 129 through 143 )
29X-RAY DIFFRACTION29chain 'D' and (resid 144 through 174 )
30X-RAY DIFFRACTION30chain 'D' and (resid 175 through 190 )
31X-RAY DIFFRACTION31chain 'D' and (resid 191 through 234 )
32X-RAY DIFFRACTION32chain 'D' and (resid 235 through 258 )
33X-RAY DIFFRACTION33chain 'E' and (resid -1 through 17 )
34X-RAY DIFFRACTION34chain 'E' and (resid 18 through 128 )
35X-RAY DIFFRACTION35chain 'E' and (resid 129 through 143 )
36X-RAY DIFFRACTION36chain 'E' and (resid 144 through 234 )
37X-RAY DIFFRACTION37chain 'E' and (resid 235 through 257 )
38X-RAY DIFFRACTION38chain 'F' and (resid -1 through 52 )
39X-RAY DIFFRACTION39chain 'F' and (resid 53 through 128 )
40X-RAY DIFFRACTION40chain 'F' and (resid 129 through 143 )
41X-RAY DIFFRACTION41chain 'F' and (resid 144 through 185 )
42X-RAY DIFFRACTION42chain 'F' and (resid 186 through 232 )
43X-RAY DIFFRACTION43chain 'F' and (resid 233 through 257 )

+
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://pdbjlvh1.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