7LVK

Cfr-modified 50S subunit from Escherichia coli


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Investigating antibiotic resistance of a ribosomal-RNA methylating enzyme through directed evolution

Tsai, K.Stojkovic, V.Noda-Garcia, L.Myasnikov, A.G.Young, I.D.Palla, A.Venkataramanan, S.Floor, S.Fraser, J.S.Frost, A.Tawfik, D.S.Fujimori, D.G.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth K]273Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth L]209Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth M]201Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth N]179Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth O]177Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth P]149Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth R]142Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth S]123Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth T]144Escherichia coliMutation(s): 0 
Gene Names: 
rplOA8C65_19395A9R57_24660ACU57_21045AM464_09135AUQ13_22145BANRA_01932BANRA_03684BHS87_18545BJJ90_02210BMA87_18510BON75_18850BON98_13310BUE81_25610BvCms2454_01416BvCmsHHP001_00334BvCmsHHP019_04131BvCmsHHP056_02703BvCmsKSP026_02554BvCmsSINP011_02480BW690_10710BZL31_22885C5F72_02595C5F73_02860C5N07_23575C9E25_20065C9Z39_20710CA593_09735CG692_20270CI693_13520CI694_01990CIG45_22410D0X26_24495D2185_22985D3821_17755D3O91_20305D3Y67_24390D4638_19455D4718_17880D9C99_17930D9D20_21995D9D44_22490D9G29_15635D9G69_20945D9H68_17710D9J52_19090D9Z28_15390DAH37_14685DBQ99_03415DJ503_19770DL326_22310DNC98_19095DT034_22410DTL43_21000E2119_19640E2134_21880E2135_06185E4A44_21305E4K51_21490E4K55_21420E4K60_18985E4K61_20025E5P22_10480E5P28_20875EA213_19860EAI42_04990EAI52_16365EC1094V2_354EC3234A_55c00230EC3426_04459ECTO6_00449ED307_17010EEP23_17135EG808_17075EI021_21030EI028_20740EI032_18995EI041_20035EIZ93_12470EL75_0396EL79_0415EL80_0407ELT20_19170EPT01_19765ERS085365_03907ERS085416_03881ERS139211_03685ERS150873_04051EXX71_21335EYD11_02080F1E19_19655F9040_18095FRV13_20015FV293_22465FWK02_06270G5632_17770G5688_20025GHR40_07050GKF39_20550GKF74_18130GKF86_20070GKF89_18470GP671_20580GP689_20785GP954_00945GP979_02005GQE33_22230GQE34_14255GQE64_20420GQM17_19915GRW05_09060GRW27_21285GRW42_19350GRW57_03540GRW80_20585GRW81_21150NCTC10963_00456NCTC11022_03475NCTC11126_02772NCTC12650_00710NCTC13216_01351NCTC9045_00567NCTC9062_02686NCTC9117_00757NCTC9706_02738PGD_00585RK56_021420SAMEA3472047_03862SAMEA3472080_04748SAMEA3484427_04887SAMEA3484429_04875SAMEA3752559_00346SAMEA3753300_02227

UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth U]136Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth V]127Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L18N [auth W]117Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth X]115Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth Y]118Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth Z]103Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth a]110Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth b]100Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L24T [auth c]104Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth d]94Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth e]85Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth f]78Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth g]63Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth h]59Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth i]57Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth j]55Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth k]46Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L35CA [auth l]65Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth m]38Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S rRNAA [auth I]2904Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S rRNAB [auth J]120Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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CH [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth I] , AC [auth I] , AD [auth I] , AE [auth I] , AF [auth I] , AG [auth I] , AH [auth L] , BB [auth I] , 
AB [auth I], AC [auth I], AD [auth I], AE [auth I], AF [auth I], AG [auth I], AH [auth L], BB [auth I], BC [auth I], BD [auth I], BE [auth I], BF [auth I], BG [auth I], BH [auth W], CB [auth I], CC [auth I], CD [auth I], CE [auth I], CF [auth I], CG [auth I], DB [auth I], DC [auth I], DD [auth I], DE [auth I], DF [auth I], DG [auth I], EA [auth I], EB [auth I], EC [auth I], ED [auth I], EE [auth I], EF [auth I], EG [auth I], FA [auth I], FB [auth I], FC [auth I], FD [auth I], FE [auth I], FF [auth I], FG [auth I], GA [auth I], GB [auth I], GC [auth I], GD [auth I], GE [auth I], GF [auth I], GG [auth I], HA [auth I], HB [auth I], HC [auth I], HD [auth I], HE [auth I], HF [auth I], HG [auth I], IA [auth I], IB [auth I], IC [auth I], ID [auth I], IE [auth I], IF [auth I], IG [auth I], JA [auth I], JB [auth I], JC [auth I], JD [auth I], JE [auth I], JF [auth I], JG [auth I], KA [auth I], KB [auth I], KC [auth I], KD [auth I], KE [auth I], KF [auth I], KG [auth I], LA [auth I], LB [auth I], LC [auth I], LD [auth I], LE [auth I], LF [auth I], LG [auth I], MA [auth I], MB [auth I], MC [auth I], MD [auth I], ME [auth I], MF [auth I], MG [auth I], NA [auth I], NB [auth I], NC [auth I], ND [auth I], NE [auth I], NF [auth I], NG [auth I], OA [auth I], OB [auth I], OC [auth I], OD [auth I], OE [auth I], OF [auth I], OG [auth I], PA [auth I], PB [auth I], PC [auth I], PD [auth I], PE [auth I], PF [auth I], PG [auth I], QA [auth I], QB [auth I], QC [auth I], QD [auth I], QE [auth I], QF [auth I], QG [auth I], RA [auth I], RB [auth I], RC [auth I], RD [auth I], RE [auth I], RF [auth I], RG [auth I], SA [auth I], SB [auth I], SC [auth I], SD [auth I], SE [auth I], SF [auth I], SG [auth I], TA [auth I], TB [auth I], TC [auth I], TD [auth I], TE [auth I], TF [auth I], TG [auth I], UA [auth I], UB [auth I], UC [auth I], UD [auth I], UE [auth I], UF [auth I], UG [auth I], VA [auth I], VB [auth I], VC [auth I], VD [auth I], VE [auth I], VF [auth I], VG [auth I], WA [auth I], WB [auth I], WC [auth I], WD [auth I], WE [auth I], WF [auth I], WG [auth I], XA [auth I], XB [auth I], XC [auth I], XD [auth I], XE [auth I], XF [auth I], XG [auth J], YA [auth I], YB [auth I], YC [auth I], YD [auth I], YE [auth I], YF [auth I], YG [auth K], ZA [auth I], ZB [auth I], ZC [auth I], ZD [auth I], ZE [auth I], ZF [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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ZG [auth K]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4D4
Query on 4D4
L [auth U]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI137270

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release