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- PDB-7vok: The Crystal structure of EF-Tu and GDP from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7vok
TitleThe Crystal structure of EF-Tu and GDP from Mycobacterium tuberculosis
ComponentsElongation factor TuEF-Tu
KeywordsElongation factor / Mycobacterium tuberculosis / Elongation factor Tu / Xray
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsZhan, B.W. / Li, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: Commun Biol / Year: 2022
Title: Structural insights of the elongation factor EF-Tu complexes in protein translation of Mycobacterium tuberculosis.
Authors: Zhan, B. / Gao, Y. / Gao, W. / Li, Y. / Li, Z. / Qi, Q. / Lan, X. / Shen, H. / Gan, J. / Zhao, G. / Li, J.
History
DepositionOct 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu
B: Elongation factor Tu
C: Elongation factor Tu
D: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,46812
Polymers174,5984
Non-polymers1,8708
Water0
1
A: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1173
Polymers43,6491
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-16 kcal/mol
Surface area17920 Å2
MethodPISA
2
B: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1173
Polymers43,6491
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-17 kcal/mol
Surface area17890 Å2
MethodPISA
3
C: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1173
Polymers43,6491
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-17 kcal/mol
Surface area17670 Å2
MethodPISA
4
D: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1173
Polymers43,6491
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-17 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.059, 75.180, 127.176
Angle α, β, γ (deg.)90.000, 93.770, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 37 or resid 45 through 396))
21(chain B and (resid 10 through 37 or resid 45 through 396))
31(chain C and (resid 10 through 37 or resid 45 through 396))
41chain D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSHISHIS(chain A and (resid 10 through 37 or resid 45 through 396))AA10 - 3710 - 37
12GLUGLULYSLYS(chain A and (resid 10 through 37 or resid 45 through 396))AA45 - 39645 - 396
21LYSLYSHISHIS(chain B and (resid 10 through 37 or resid 45 through 396))BB10 - 3710 - 37
22GLUGLULYSLYS(chain B and (resid 10 through 37 or resid 45 through 396))BB45 - 39645 - 396
31LYSLYSHISHIS(chain C and (resid 10 through 37 or resid 45 through 396))CC10 - 3710 - 37
32GLUGLULYSLYS(chain C and (resid 10 through 37 or resid 45 through 396))CC45 - 39645 - 396
41LYSLYSLYSLYSchain DDD10 - 39610 - 396

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Components

#1: Protein
Elongation factor Tu / EF-Tu / EF-Tu


Mass: 43649.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: tuf_1, tuf, C0094_03695, DSI38_24795, E5M05_06550, E5M52_05390, E5M78_06185, ERS007657_00720, ERS007663_01319, ERS007670_02372, ERS007703_04298, ERS007720_00657, ERS007722_02966, ERS013471_ ...Gene: tuf_1, tuf, C0094_03695, DSI38_24795, E5M05_06550, E5M52_05390, E5M78_06185, ERS007657_00720, ERS007663_01319, ERS007670_02372, ERS007703_04298, ERS007720_00657, ERS007722_02966, ERS013471_00592, ERS023446_00428, ERS024276_01766, ERS027646_00039, ERS027659_02599, ERS027661_00652, ERS094182_01322, F6W99_03360, GCL30_03260, SAMEA2683035_02505
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IWT1
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG 6000, 100mM N-2-hydroxyethylpiperazine-N-ethane-sulphonicacid pH 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 23713 / % possible obs: 94.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 53.01 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.043 / Rrim(I) all: 0.104 / Χ2: 0.941 / Net I/σ(I): 7.9 / Num. measured all: 109018
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.522.90.31722410.6330.2010.3780.83890.7
3.52-3.663.30.29123060.8320.1720.3410.89893.2
3.66-3.833.50.24723120.8980.1380.2850.94493.7
3.83-4.033.60.20522910.9360.1130.2360.99992.3
4.03-4.284.30.15223350.980.0740.171.0693.5
4.28-4.615.20.13124070.9910.060.1451.05796.9
4.61-5.075.50.1124550.9910.0480.1211.03597.9
5.07-5.85.30.10824300.9880.0490.1190.97196.9
5.8-7.295.70.08524270.9920.0360.0930.8596.5
7.29-306.40.06725090.9940.0280.0730.78796.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFC

1efc


Resolution: 3.4→29.95 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 31.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3016 1017 5.08 %
Rwork0.2443 18993 -
obs0.2473 20010 80.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.24 Å2 / Biso mean: 53.4876 Å2 / Biso min: 7.76 Å2
Refinement stepCycle: final / Resolution: 3.4→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11796 0 116 0 11912
Biso mean--64.92 --
Num. residues----1529
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4604X-RAY DIFFRACTION7.453TORSIONAL
12B4604X-RAY DIFFRACTION7.453TORSIONAL
13C4604X-RAY DIFFRACTION7.453TORSIONAL
14D4604X-RAY DIFFRACTION7.453TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.580.3221450.2746978102329
3.58-3.80.33691050.27691927203257
3.8-4.090.33241550.27152904305987
4.09-4.50.31451730.23833258343196
4.5-5.150.30381640.22883291345597
5.15-6.480.3021680.27563286345496
6.48-29.950.26442070.213349355697
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)
10.5472-0.0701-0.10420.32530.05710.31920.12410.12080.05640.0803-0.11870.3246-0.1841-0.17610.0860.11260.31350.0799-0.1153-0.35290.0567-2.7926-25.212344.1057
21.5503-0.465-0.14223.21560.1582.7967-0.074-0.4058-0.12780.42950.09480.47570.2873-0.454-0.03590.5682-0.0561-0.08610.6296-0.05250.2184-20.9052-25.825279.8178
30.27120.03260.13850.34320.26680.7143-0.0518-0.16820.05970.0454-0.02530.06590.0655-0.1012-0.11040.3521-0.1178-0.05510.3337-0.28120.20065.4401-20.941571.9759
41.7144-0.09080.23351.2223-0.18471.8917-0.0794-0.7237-0.27310.2583-0.09550.40550.2978-0.19430.20360.50150.15760.11630.5952-0.10670.3017-46.0818-24.009318.1063
52.8371-0.6503-0.59622.1621-0.2364.5592-0.28540.61490.2568-0.1340.06560.3623-0.4165-0.46410.19280.4555-0.1096-0.0490.49680.05180.6579-64.3381-22.3916-17.603
62.2943-0.22660.32590.91570.15152.00320.03030.34570.3521-0.0884-0.1517-0.1835-0.1417-0.09560.03210.12370.0663-0.07990.2878-0.07380.5383-37.7453-26.2565-10.2045
72.56360.2440.76651.1840.18371.1187-0.1830.52520.15920.0623-0.0762-0.0037-0.11310.13130.13450.4469-0.16480.00410.2419-0.02550.26550.3414-12.7489-15.2383
82.1520.83310.35032.64920.49312.88730.0343-0.25710.25740.33480.16020.31720.0596-0.5313-0.1080.24040.06980.00790.511-0.08060.2791-18.3453-8.712119.8893
91.72110.5892-0.00411.48960.11481.7174-0.0826-0.05450.5890.0181-0.2036-0.47440.0608-0.14330.17780.26650.0926-0.1550.2479-0.05720.51278.2652-5.117312.2655
101.48280.2945-0.13530.7311-0.56291.7158-0.1060.97150.0901-0.7137-0.15380.08390.0151-0.31580.31571.07650.0877-0.0610.7708-0.05060.5729-51.74973.144546.8364
113.05780.34320.48283.0147-0.60094.3567-0.0447-0.4129-0.0578-0.0237-0.3081-0.12610.26390.01730.33460.2669-0.07860.00450.26720.0150.2775-33.9004-2.084882.3266
122.55060.65040.89120.31660.22352.18530.13-0.24020.05880.3436-0.1340.1013-0.03330.0971-0.040.4218-0.0007-0.12730.445-0.15320.4516-60.3898-5.014673.3808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 10:205)A10 - 205
2X-RAY DIFFRACTION2(chain A and resseq 211:303)A211 - 303
3X-RAY DIFFRACTION3(chain A and resseq 304:396)A304 - 396
4X-RAY DIFFRACTION4(chain B and resseq 10:205)B10 - 205
5X-RAY DIFFRACTION5(chain B and resseq 211:303)B211 - 303
6X-RAY DIFFRACTION6(chain B and resseq 304:396)B304 - 396
7X-RAY DIFFRACTION7(chain C and resseq 10:205)C10 - 205
8X-RAY DIFFRACTION8(chain C and resseq 211:303)C211 - 303
9X-RAY DIFFRACTION9(chain C and resseq 304:396)C304 - 396
10X-RAY DIFFRACTION10(chain D and resseq 10:205)D10 - 205
11X-RAY DIFFRACTION11(chain D and resseq 211:303)D211 - 303
12X-RAY DIFFRACTION12(chain D and resseq 304:396)D304 - 396

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