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- PDB-2mzw: Staphylococcus aureus FusB:EF-GC3 complex -

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Basic information

Entry
Database: PDB / ID: 2mzw
TitleStaphylococcus aureus FusB:EF-GC3 complex
Components
  • Elongation factor G
  • Far1
KeywordsTRANSLATION/ANTIBIOTIC RESISTANCE / antibiotic resistance / METAL BINDING PROTEIN / TRANSLATION-ANTIBIOTIC RESISTANCE complex
Function / homology
Function and homology information


ribosome disassembly / translation elongation factor activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Monooxygenase - #250 / Elongation factor G-binding protein, N-terminal / Elongation factor G-binding protein, C-terminal treble-clef zinc-finger / EF-G binding protein, N-terminal domain superfamily / Elongation factor G-binding protein, N-terminal / FBP C-terminal treble-clef zinc-finger / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / : ...Monooxygenase - #250 / Elongation factor G-binding protein, N-terminal / Elongation factor G-binding protein, C-terminal treble-clef zinc-finger / EF-G binding protein, N-terminal domain superfamily / Elongation factor G-binding protein, N-terminal / FBP C-terminal treble-clef zinc-finger / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Monooxygenase / Ribosomal Protein S5; domain 2 - #10 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal Protein S5; domain 2 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor G / Far1 / Elongation factor G
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsTomlinson, J.H. / Thompson, G.S. / Kalverda, A.P. / Zhuravleva, A. / O'Neill, A.
CitationJournal: Sci Rep / Year: 2016
Title: A target-protection mechanism of antibiotic resistance at atomic resolution: insights into FusB-type fusidic acid resistance.
Authors: Tomlinson, J.H. / Thompson, G.S. / Kalverda, A.P. / Zhuravleva, A. / O'Neill, A.J.
History
DepositionFeb 25, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor G
B: Far1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8923
Polymers60,8262
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-6.2 kcal/mol
Surface area28490 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Elongation factor G / EF-G


Mass: 33472.766 Da / Num. of mol.: 1 / Fragment: Domains III-V, residues 401-692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: CH51_02860, CH52_03020, DA92_03395, DP18_1097, EX97_02750, fusA, SAU060112_10722, SAXN108_0601, X998_0588
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: W8UT26, UniProt: Q2G0N1*PLUS
#2: Protein Far1 / FusB / FusB protein / Fusidic acid resistance


Mass: 27353.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: far1, fusB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q8GNY5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: A structural model of the complex between the fusidic acid resistance protein FusB and a truncated form of EF-G. This model was produced using NMR data to dock X-ray structures.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1232D 1H-15N TROSY-HSQC
1342D 1H-15N TROSY-HSQC
1452D 1H-15N TROSY-HSQC
1513D HNCA
1613D HN(CO)CA
1772D 1H-15N HSQC/HMQC
1882D 1H-15N HSQC/HMQC
1992D 1H-15N HSQC/HMQC
110102D 1H-15N HSQC/HMQC
111112D 1H-15N HSQC/HMQC
11222D 1H-15N HSQC (ARTSY)
11352D 1H-15N HSQC (ARTSY)
114182D 1H-15N HSQC (ARTSY)
115133D TROSY-HNCO
116133D TROSY-HNCA
117133D TROSY-HN(CO)CA
118143D TROSY-HNCO
119143D TROSY-HNCA
120143D TROSY-HN(CO)CA
121153D TROSY-HNCO
122153D TROSY-HNCA
123153D TROSY-HN(CO)CA
124163D TROSY-HNCO
125163D TROSY-HNCA
126163D TROSY-HN(CO)CA
127173D TROSY-HNCO
128173D TROSY-HNCA
129173D TROSY-HN(CO)CA
130162D 1H-15N HSQC 1H R1 relaxation series (saturation recovery)

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.250 mM [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)] EF-GC3, 0.375 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2Osample190% H2O/10% D2O
solution20.250 mM [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)] EF-GC3, 0.375 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 6 mg/mL Pf1 phage, 90% H2O/10% D2Osample290% H2O/10% D2O
solution30.250 mM [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)] EF-GC3, 0.375 mM FusB R19C mutant tagged with MTSL, 20 mM TRIS, 300 mM sodium chloride, 90% H2O/10% D2Osample390% H2O/10% D2O
solution40.250 mM [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)] EF-GC3, 0.375 mM FusB T26C mutant tagged with MTSL, 20 mM TRIS, 300 mM sodium chloride, 90% H2O/10% D2Osample490% H2O/10% D2O
solution50.250 mM [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)] EF-GC3, 0.375 mM FusB N150C mutant tagged with MTSL, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 6 mg/mL Pf1 phage, 90% H2O/10% D2Osample590% H2O/10% D2O
solution60.250 mM [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H carbon source)] EF-GC3, 0.375 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 0-1 (titration: 0.25 mM steps) mM Gd-DPTA-BMA, 90% H2O/10% D2Osample690% H2O/10% D2O
solution70.30 mM [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance lysine ] EF-GC3, 0.45 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2Osample790% H2O/10% D2O
solution80.30 mM [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance valine ] EF-GC3, 0.45 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2Osample890% H2O/10% D2O
solution90.30 mM [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance phenylalanine ] EF-GC3, 0.45 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2Osample990% H2O/10% D2O
solution100.30 mM [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance alanine ] EF-GC3, 0.45 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2Osample1090% H2O/10% D2O
solution110.30 mM [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance asparagine ] EF-GC3, 0.45 mM FusB, 20 mM TRIS, 300 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2Osample1190% H2O/10% D2O
solution120.3 mM FusB [U-100% 15N, partial 2H], 0.45 mM EF-GC3, 20 mM TrisHCl, 300 mM NaCl, 5 mM DTT, 90% H2O/10% D2Osample1290% H2O/10% D2O
solution130.3 mM FusB [U-100% 15N, partial 2H, 100% natural abundance lysine], 0.45 mM EF-GC3, 20 mM TrisHCl, 300 mM NaCl, 5 mM DTT, 90% H2O/10% D2Osample1390% H2O/10% D2O
solution140.3 mM FusB [U-100% 15N, partial 2H, 100% natural abundance leucine], 0.45 mM EF-GC3, 20 mM TrisHCl, 300 mM NaCl, 5 mM DTT, 90% H2O/10% D2Osample1490% H2O/10% D2O
solution150.3 mM FusB [U-100% 15N, partial 2H, 100% natural abundance phenylalanine], 0.45 mM EF-GC3, 20 mM TrisHCl, 300 mM NaCl, 5 mM DTT, 90% H2O/10% D2Osample1590% H2O/10% D2O
solution160.3 mM FusB [U-100% 15N, partial 2H, 100% natural abundance valine], 0.45 mM EF-GC3, 20 mM TrisHCl, 300 mM NaCl, 5 mM DTT, 90% H2O/10% D2Osample1690% H2O/10% D2O
solution170.3 mM FusB [U-100% 15N, partial 2H, 100% natural abundance asparagine], 0.45 mM EF-GC3, 20 mM TrisHCl, 300 mM NaCl, 5 mM DTT, 90% H2O/10% D2Osample1790% H2O/10% D2O
solution180.3 mM FusB [U-100% 15N, partial 2H], 0.45 mM EF-GC3, 20 mM TrisHCl, 300 mM NaCl, 5 mM DTT, 6mg/ml Pf1 phage, 90% H2O/10% D2Osample1890% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.250 mMEF-GC3[U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)]1
0.375 mMFusBnatural abundance1
20 mMTRISnatural abundance1
300 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
0.250 mMEF-GC3[U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)]2
0.375 mMFusBnatural abundance2
20 mMTRISnatural abundance2
300 mMsodium chloridenatural abundance2
5 mMDTTnatural abundance2
6 mg/mLPf1 phagenatural abundance2
0.250 mMEF-GC3[U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)]3
0.375 mMFusB R19C mutant tagged with MTSLnatural abundance3
20 mMTRISnatural abundance3
300 mMsodium chloridenatural abundance3
0.250 mMEF-GC3[U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)]4
0.375 mMFusB T26C mutant tagged with MTSLnatural abundance4
20 mMTRISnatural abundance4
300 mMsodium chloridenatural abundance4
0.250 mMEF-GC3[U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)]5
0.375 mMFusB N150C mutant tagged with MTSLnatural abundance5
20 mMTRISnatural abundance5
300 mMsodium chloridenatural abundance5
5 mMDTTnatural abundance5
6 mg/mLPf1 phage5
0.250 mMEF-GC3[U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H carbon source)]6
0.375 mMFusBnatural abundance6
20 mMTRISnatural abundance6
300 mMsodium chloridenatural abundance6
mMGd-DPTA-BMAnatural abundance0-16
0.30 mMEF-GC3[U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance lysine ]7
0.45 mMFusBnatural abundance7
20 mMTRISnatural abundance7
300 mMsodium chloridenatural abundance7
5 mMDTTnatural abundance7
0.30 mMEF-GC3[U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance valine ]8
0.45 mMFusBnatural abundance8
20 mMTRISnatural abundance8
300 mMsodium chloridenatural abundance8
5 mMDTTnatural abundance8
0.30 mMEF-GC3[U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance phenylalanine ]9
0.45 mMFusBnatural abundance9
20 mMTRISnatural abundance9
300 mMsodium chloridenatural abundance9
5 mMDTTnatural abundance9
0.30 mMEF-GC3[U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance alanine ]10
0.45 mMFusBnatural abundance10
20 mMTRISnatural abundance10
300 mMsodium chloridenatural abundance10
5 mMDTTnatural abundance10
0.30 mMEF-GC3[U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance asparagine ]11
0.45 mMFusBnatural abundance11
20 mMTRISnatural abundance11
300 mMsodium chloridenatural abundance11
5 mMDTTnatural abundance11
0.30 mMFusBFusB[U-100% 15N, partial 2H]12
0.45 mMEF-GC3natural abundance12
20 mMTrisHClnatural abundance12
300 mMsodium chloridenatural abundance12
5 mMDTTnatural abundance12
0.30 mMFusB[U-100% 15N, partial 2H, 100% natural abundance lysine]13
0.45 mMEF-GC3natural abundance13
20 mMTrisHClnatural abundance13
300 mMsodium chloridenatural abundance13
5 mMDTTnatural abundance13
0.30 mMFusB[U-100% 15N, partial 2H, 100% natural abundance leucine]14
0.45 mMEF-GC3natural abundance14
20 mMTrisHClnatural abundance14
300 mMsodium chloridenatural abundance14
5 mMDTTnatural abundance14
0.30 mMFusB[U-100% 15N, partial 2H, 100% natural abundance phenylalanine]15
0.45 mMEF-GC3natural abundance15
20 mMTrisHClnatural abundance15
300 mMsodium chloridenatural abundance15
5 mMDTTnatural abundance15
0.30 mMFusB[U-100% 15N, partial 2H, 100% natural abundance valine]16
0.45 mMEF-GC3natural abundance16
20 mMTrisHClnatural abundance16
300 mMsodium chloridenatural abundance16
5 mMDTTnatural abundance16
0.30 mMFusB[U-100% 15N, partial 2H, 100% natural abundance asparagine]17
0.45 mMEF-GC3natural abundance17
20 mMTrisHClnatural abundance17
300 mMsodium chloridenatural abundance17
5 mMDTTnatural abundance17
0.30 mMFusB[U-100% 15N, partial 2H]18
0.45 mMEF-GC3natural abundance18
20 mMTrisHClnatural abundance18
300 mMsodium chloridenatural abundance18
5 mMDTTnatural abundance18
6 mg/mLPf1 phagenatural abundance18
Sample conditionsIonic strength: 0.3 / pH: 8 / Pressure: 1.000 atm / Temperature: 298.150 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA7501
Agilent InovaAgilentINOVA6002
Varian InovaVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.1CCPNchemical shift assignment
CcpNmr Analysis2.1CCPNprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView7.9Johnson, One Moon Scientificprocessing
NMRView7.9Johnson, One Moon Scientificdata analysis
X-PLOR NIH2.33.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.33.0Schwieters, Kuszewski, Tjandra and Clorerefinement
HADDOCK2.1Alexandre Bonvinstructure solution
HADDOCK2.1Alexandre Bonvindocking based on nmr restraints
HADDOCK2.1Alexandre Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 8
Details: Reorientation of helices in domain IV and domain reorientation as rigid bodies refined to RDCs and solvent PREs, Semi-rigid docking of structures driven by RDCs, ambiguous distance ...Details: Reorientation of helices in domain IV and domain reorientation as rigid bodies refined to RDCs and solvent PREs, Semi-rigid docking of structures driven by RDCs, ambiguous distance restraints from chemical shift perturbations and distance restraints based on PREs.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 1

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