[English] 日本語
Yorodumi
- PDB-6cyn: CTX-M-14 N106S/D240G mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cyn
TitleCTX-M-14 N106S/D240G mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase CTX-M-14
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPatel, M.P. / Hu, L. / Sankaran, B. / Brown, C. / Prasad, B.V.V. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI32956 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Synergistic effects of functionally distinct substitutions in beta-lactamase variants shed light on the evolution of bacterial drug resistance.
Authors: Patel, M.P. / Hu, L. / Brown, C.A. / Sun, Z. / Adamski, C.J. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionApr 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.5Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
E: Beta-lactamase
F: Beta-lactamase
G: Beta-lactamase
H: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)223,3248
Polymers223,3248
Non-polymers00
Water61,3413405
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.238, 83.238, 231.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Beta-lactamase /


Mass: 27915.482 Da / Num. of mol.: 8 / Mutation: N106S, D240G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, BK334_27290, BMR21_24310, BMR35_25520, BMR49_25760, BXT93_06855, CA268_29135, CDL37_21060, CR538_26855, ETN48_p0088, pCT_085, pHK01_011
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9L5C7, UniProt: Q9L5C8*PLUS, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3405 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25% PEG 1500 (w/v), 0.1 M PCB buffer, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 235349 / % possible obs: 99.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.662

-
Processing

Software
NameVersionClassification
PHENIX(DEV_3071: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT
Resolution: 1.6→34.42 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.21
RfactorNum. reflection% reflection
Rfree0.204 11682 4.96 %
Rwork0.168 --
obs0.169 235349 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15500 0 0 3405 18905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615882
X-RAY DIFFRACTIONf_angle_d0.8121644
X-RAY DIFFRACTIONf_dihedral_angle_d15.7849674
X-RAY DIFFRACTIONf_chiral_restr0.0492575
X-RAY DIFFRACTIONf_plane_restr0.0062851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6008-1.6190.28053710.19777318X-RAY DIFFRACTION99
1.619-1.63810.25493640.18997487X-RAY DIFFRACTION100
1.6381-1.65810.21734200.18917551X-RAY DIFFRACTION100
1.6581-1.6790.23834040.1947412X-RAY DIFFRACTION100
1.679-1.70110.23763920.19477501X-RAY DIFFRACTION100
1.7011-1.72440.22553780.18297461X-RAY DIFFRACTION100
1.7244-1.74910.22264000.18137497X-RAY DIFFRACTION100
1.7491-1.77520.21554300.18627498X-RAY DIFFRACTION100
1.7752-1.80290.22123860.17827473X-RAY DIFFRACTION100
1.8029-1.83250.20313860.17767472X-RAY DIFFRACTION100
1.8325-1.86410.19143870.17437444X-RAY DIFFRACTION100
1.8641-1.8980.21714260.17347520X-RAY DIFFRACTION100
1.898-1.93450.21614720.18127389X-RAY DIFFRACTION100
1.9345-1.9740.21824070.17637456X-RAY DIFFRACTION100
1.974-2.01690.19153240.1587558X-RAY DIFFRACTION100
2.0169-2.06380.19613950.15117454X-RAY DIFFRACTION100
2.0638-2.11540.17324210.15717479X-RAY DIFFRACTION100
2.1154-2.17260.18693460.15377457X-RAY DIFFRACTION100
2.1726-2.23650.20123360.15897552X-RAY DIFFRACTION100
2.2365-2.30870.20823510.167541X-RAY DIFFRACTION100
2.3087-2.39120.21464530.1657437X-RAY DIFFRACTION100
2.3912-2.48690.18824600.16067376X-RAY DIFFRACTION100
2.4869-2.60.2014180.15897504X-RAY DIFFRACTION99
2.6-2.7370.18093630.16167420X-RAY DIFFRACTION100
2.737-2.90840.21213480.17057518X-RAY DIFFRACTION99
2.9084-3.13290.1823850.16457461X-RAY DIFFRACTION99
3.1329-3.44790.18893560.15647511X-RAY DIFFRACTION99
3.4479-3.94620.17954150.14947423X-RAY DIFFRACTION99
3.9462-4.96940.20913710.15687377X-RAY DIFFRACTION98
4.9694-34.42760.2493170.21197120X-RAY DIFFRACTION94
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)
13.50810.35031.28081.11180.00011.71480.072-0.30260.25780.3258-0.0240.0656-0.7223-0.1571-0.0460.31060.00640.06710.2066-0.03410.119824.800728.9072-7.5164
21.82040.88350.4361.00340.63231.1801-0.0164-0.04990.1348-0.0519-0.01410.0933-0.2839-0.24180.01630.12290.03680.01640.12850.01780.096715.979222.8876-22.3135
38.2684-4.37582.46745.3197-1.80622.05360.3060.4724-0.3568-0.3974-0.18010.41820.3242-0.2897-0.14210.2026-0.0849-0.01950.24250.01360.10578.52711.9889-33.6658
41.27520.41160.37710.68670.39731.90610.0408-0.14040.02410.0459-0.02870.0484-0.0297-0.3037-0.02210.05550.0080.0160.13910.01290.085415.070614.1905-22.249
53.6685-0.94610.36682.2951-0.39950.1252-0.0173-0.08310.2530.2639-0.07070.2682-0.1124-0.450.08650.17450.04790.04090.3347-0.0560.138513.141824.7743-11.0828
66.9211-1.8573-3.53893.73561.68265.2407-0.0436-0.7245-0.20790.22910.06720.0356-0.18970.0326-0.02940.1144-0.0129-0.02570.22480.01130.057325.959518.195-7.0247
74.3824-0.47811.35791.0029-0.50512.09440.0187-0.20180.28670.1761-0.020.0293-0.3828-0.08160.01180.12390.00160.02870.098-0.01380.0884.163364.9776-7.2691
81.51130.80730.66030.76620.45441.4411-0.03230.00020.0425-0.03090.02830.0336-0.124-0.1366-0.00810.06860.01630.00980.0870.01930.0816-4.771858.8988-22.2934
96.2977-4.46773.24476.6768-2.51662.76490.27750.5176-0.4236-0.4192-0.1590.53790.3532-0.276-0.14070.1558-0.0736-0.01820.21330.01530.1288-12.642738.1516-33.715
100.63140.2170.11210.35250.0811.18610.0348-0.0238-0.00590.02980.00260.030.0353-0.1703-0.04050.0454-0.00110.00660.09510.01210.0841-5.524450.1292-22.222
111.96780.3750.48341.6509-0.24990.2512-0.1143-0.10290.0390.24420.04820.2532-0.0728-0.31850.06150.11460.04640.03260.2328-0.01430.1064-7.321860.5977-11.2515
126.9176-1.9652-2.95662.33370.98144.7288-0.1178-0.6623-0.16950.19950.12210.00770.11030.1233-0.00760.0568-0.0223-0.02540.13050.00440.07454.588454.3802-6.7574
131.4790.60640.67490.70390.42882.3130.0286-0.03730.1416-0.0041-0.01420.0508-0.4286-0.0377-0.0210.150.01270.04720.07880.00340.103139.93261.0355-16.4437
144.8141-3.16392.44854.9242-1.95492.69130.28720.4807-0.1403-0.5252-0.18170.20940.3605-0.328-0.10050.1716-0.04210.01780.21430.00490.090329.496837.888-34.1
150.99410.5036-0.58562.1245-0.51782.35550.00240.0187-0.09410.0178-0.0259-0.05620.1672-0.1070.01640.049-0.00940.00350.0845-0.0050.07335.792441.6326-27.3857
163.5326-0.1239-0.04771.37791.08632.29020.0577-0.00220.2524-0.12460.0167-0.2045-0.20320.1343-0.07060.0767-0.02110.02810.0788-0.01130.08247.363953.0381-27.5398
170.77760.31560.66250.5586-0.08831.93510.0055-0.14930.07480.03120.01660.1135-0.2206-0.2945-0.02410.08210.03860.02930.1296-0.00840.10632.621155.4935-15.637
188.0129-2.1691-2.40132.6498-0.08153.5917-0.2848-0.397-0.19420.32930.3064-0.0114-0.12680.4525-0.04380.0708-0.015-0.02160.1466-0.02960.057946.454154.0776-6.9433
191.57980.77381.19340.58010.44691.901-0.0517-0.09530.1008-0.0137-0.02080.0833-0.3151-0.2130.05580.11340.04230.02330.09520.0040.094118.911697.0765-16.4996
207.5099-5.06953.12047.2241-2.33872.77290.30460.556-0.1492-0.4405-0.26080.19710.1786-0.2574-0.05790.1385-0.00630.01480.19160.00970.07498.679273.8327-34.1445
211.732-0.5731-0.55693.64781.17052.54550.0234-0.0874-0.05670.1286-0.0304-0.19860.23090.05120.00180.0991-0.02580.00250.1060.02960.100213.849171.7985-23.9703
220.9640.34770.67280.61220.37361.34610.0208-0.13730.08180.0206-0.01860.0265-0.0505-0.2002-0.00860.05470.0090.01530.09930.00370.084415.539988.9368-21.8589
232.9943-0.3020.39382.0859-0.56630.6832-0.1102-0.20270.08340.3318-0.01340.42070.0068-0.50610.130.11040.02770.05760.3233-0.07290.14912.676896.0125-11.1235
249.0638-1.7156-2.97162.78850.82135.1239-0.1802-0.4435-0.17640.23030.18040.0380.14890.07520.00490.0626-0.0144-0.02530.1012-0.00460.049225.841990.4004-7.2196
251.75590.96040.15312.40921.04811.30440.00510.41320.1796-0.30280.0410.2345-0.5402-0.5716-0.04550.25360.06060.0010.30190.07630.13073.9989.1289-70.2653
262.00970.91110.86640.9190.11641.2471-0.0561-0.04730.1195-0.01170.02180.0631-0.3234-0.11070.02620.15290.01520.02630.08710.00310.092113.805393.7111-55.3222
271.9036-1.2314-0.67369.55524.31972.40720.0548-0.32110.22710.53850.1978-0.6547-0.18360.5202-0.27870.2158-0.08740.00520.2886-0.05050.135135.376990.8215-43.608
281.09990.20180.15430.7162-0.20941.66120.020.04180.06450.00480.038-0.0439-0.24690.0891-0.06250.1233-0.02850.02420.0646-0.00720.088622.338989.4851-51.8198
291.40350.07180.57430.70060.42270.4621-0.25370.39920.1625-0.35180.2422-0.0942-0.28520.1319-0.01220.2667-0.09690.00590.16220.0270.115419.980691.5993-66.8575
301.89580.7482-0.12713.79090.59240.1743-0.0320.19360.3623-0.2002-0.02420.0209-0.49840.20010.0580.3813-0.0633-0.02340.14640.06990.151713.570297.1173-66.568
313.68221.5621-0.91129.1216-3.63595.663-0.16330.3404-0.0542-0.77250.2094-0.2502-0.1143-0.2132-0.01990.1706-0.0519-0.00660.1451-0.02420.054112.994583.4797-70.893
321.30521.29980.08813.95871.19432.0673-0.06070.19280.1324-0.17580.03730.2262-0.2526-0.27030.03950.10580.0023-0.01260.12130.02960.081524.888952.9025-70.3785
331.48830.77410.54080.70150.27361.2155-0.011-0.03610.0787-0.0363-0.020.0341-0.2007-0.02860.0230.11440.00240.01190.0595-0.00520.082934.627157.6106-55.3609
342.2889-2.0787-0.49759.66763.73532.6406-0.0114-0.20380.24060.50170.1499-0.6488-0.09520.4635-0.14920.1307-0.05390.00480.2407-0.02240.103756.50254.125-43.9146
350.79070.17590.21760.38370.1421.4264-0.01420.06830.0345-0.03330.0221-0.0208-0.15970.1244-0.01290.087-0.02910.00860.05380.00440.077541.806754.5811-56.5185
361.55651.05-0.48217.4708-3.03334.2825-0.1620.1978-0.0784-0.64610.1183-0.10870.1220.06150.03150.0972-0.0393-0.02210.1006-0.02510.066133.889447.1863-70.8736
371.1486-0.22520.22794.22131.1962.30880.10140.18810.0595-0.084-0.11860.2216-0.1919-0.61180.00270.09980.02630.02040.25750.06350.10884.364417.3799-70.258
383.0510.27870.6862.13290.97090.7422-0.053-0.04260.2115-0.07120.05980.186-0.2876-0.3404-0.00160.14960.0510.02930.16770.02360.10386.040121.5892-61.1405
391.4395-0.4902-0.17951.58710.21511.7117-0.0729-0.14050.10030.1620.086-0.0473-0.29460.2031-0.02470.1478-0.0380.02260.09940.01430.078329.572619.6499-46.1763
402.4855-0.3159-0.91110.7229-0.16052.254-0.01290.0286-0.1080.022-0.0248-0.0434-0.02250.16710.03280.0809-0.02160.00570.07160.00430.084329.280613.8386-50.2399
411.3938-0.10980.38113.1764-1.0091.91520.0036-0.09610.00510.05450.09390.2277-0.1352-0.2495-0.09720.07050.01030.01760.0990.01370.071913.095615.1163-52.2104
420.82820.45310.35490.63950.95671.4994-0.02920.08730.1225-0.08940.06280.0294-0.34540.0329-0.03390.1777-0.02480.0130.06850.03110.110220.47423.4227-63.4494
432.40181.6434-1.37438.7077-2.49184.04930.10070.1754-0.0444-0.4563-0.0566-0.07280.2264-0.3945-0.05190.1-0.0369-0.03390.10680.00880.060313.018311.2552-70.678
441.22250.83890.83220.77650.81951.7351-0.06080.00330.1339-0.05730.00170.086-0.2951-0.15470.04050.1290.02770.01610.07510.02140.1089-10.297156.1888-61.177
452.356-1.3937-0.47062.8401-0.69112.3258-0.0139-0.0343-0.03110.1410.0308-0.0424-0.02530.249-0.06140.0658-0.02630.01770.11270.00010.086714.469750.1852-49.8274
460.94260.22140.62110.41090.54041.5001-0.06170.08750.0901-0.12320.07320.051-0.24230.0601-0.02510.1076-0.01820.01080.05980.02020.0949-2.097455.6846-56.9926
472.71041.4284-0.74679.2677-3.35645.02390.03010.1129-0.0785-0.5582-0.0089-0.2260.17630.1015-0.01630.0889-0.0282-0.01610.089-0.02140.0546-7.658647.0834-70.6041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 26 THROUGH 50 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 51 THROUGH 86 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 87 THROUGH 101 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 102 THROUGH 251 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 252 THROUGH 266 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 267 THROUGH 289 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 26 THROUGH 50 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 51 THROUGH 86 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 87 THROUGH 101 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 102 THROUGH 251 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 252 THROUGH 266 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 267 THROUGH 289 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 26 THROUGH 86 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 87 THROUGH 101 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 102 THROUGH 155 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 156 THROUGH 179 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 180 THROUGH 266 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 267 THROUGH 289 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 26 THROUGH 86 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 87 THROUGH 101 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 102 THROUGH 129 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 130 THROUGH 251 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 252 THROUGH 266 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 267 THROUGH 289 )
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 26 THROUGH 50 )
26X-RAY DIFFRACTION26CHAIN 'E' AND (RESID 51 THROUGH 86 )
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESID 87 THROUGH 101 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 102 THROUGH 212 )
29X-RAY DIFFRACTION29CHAIN 'E' AND (RESID 213 THROUGH 251 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 252 THROUGH 266 )
31X-RAY DIFFRACTION31CHAIN 'E' AND (RESID 267 THROUGH 289 )
32X-RAY DIFFRACTION32CHAIN 'F' AND (RESID 26 THROUGH 50 )
33X-RAY DIFFRACTION33CHAIN 'F' AND (RESID 51 THROUGH 86 )
34X-RAY DIFFRACTION34CHAIN 'F' AND (RESID 87 THROUGH 101 )
35X-RAY DIFFRACTION35CHAIN 'F' AND (RESID 102 THROUGH 266 )
36X-RAY DIFFRACTION36CHAIN 'F' AND (RESID 267 THROUGH 289 )
37X-RAY DIFFRACTION37CHAIN 'G' AND (RESID 26 THROUGH 50 )
38X-RAY DIFFRACTION38CHAIN 'G' AND (RESID 51 THROUGH 68 )
39X-RAY DIFFRACTION39CHAIN 'G' AND (RESID 69 THROUGH 101 )
40X-RAY DIFFRACTION40CHAIN 'G' AND (RESID 102 THROUGH 155 )
41X-RAY DIFFRACTION41CHAIN 'G' AND (RESID 156 THROUGH 194 )
42X-RAY DIFFRACTION42CHAIN 'G' AND (RESID 195 THROUGH 266 )
43X-RAY DIFFRACTION43CHAIN 'G' AND (RESID 267 THROUGH 289 )
44X-RAY DIFFRACTION44CHAIN 'H' AND (RESID 26 THROUGH 86 )
45X-RAY DIFFRACTION45CHAIN 'H' AND (RESID 87 THROUGH 129 )
46X-RAY DIFFRACTION46CHAIN 'H' AND (RESID 130 THROUGH 266 )
47X-RAY DIFFRACTION47CHAIN 'H' AND (RESID 267 THROUGH 288 )

+
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