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- PDB-6j7m: Complex structure of the Pseudomonas aeruginosa rhamnosyltransfer... -

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Basic information

Entry
Database: PDB / ID: 6j7m
TitleComplex structure of the Pseudomonas aeruginosa rhamnosyltransferase EarP with the acceptor elongation factor EF-P
Components
  • Earp
  • Elongation factor P
KeywordsTRANSFERASE / rhamnosyltransferase
Function / homology
Function and homology information


protein-arginine rhamnosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / translation elongation factor activity / cytosol / cytoplasm
Similarity search - Function
Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Translation elongation factor P/YeiP, central / Translation elongation factor P / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal / Elongation factor P (EF-P) OB domain ...Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Translation elongation factor P/YeiP, central / Translation elongation factor P / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal / Elongation factor P (EF-P) OB domain / Translation elongation factor, KOW-like / Elongation factor P (EF-P) KOW-like domain / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / Protein-arginine rhamnosyltransferase / Elongation factor P
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsHe, C. / Li, F.
CitationJournal: J.Bacteriol. / Year: 2019
Title: Complex Structure ofPseudomonas aeruginosaArginine Rhamnosyltransferase EarP with Its Acceptor Elongation Factor P.
Authors: He, C. / Liu, N. / Li, F. / Jia, X. / Peng, H. / Liu, Y. / Xiao, Y.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Earp
C: Earp
M: Elongation factor P
N: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,0428
Polymers137,0534
Non-polymers9894
Water6,377354
1
A: Earp
M: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0214
Polymers68,5272
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-21 kcal/mol
Surface area23940 Å2
MethodPISA
2
C: Earp
N: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0214
Polymers68,5272
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-23 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.452, 56.736, 132.419
Angle α, β, γ (deg.)90.000, 125.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Earp


Mass: 45060.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA2852 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZZ1
#2: Protein Elongation factor P / / EF-P


Mass: 23466.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: efp / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZZ2
#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium sulfate, 0.1 M MES pH 6.5, 20% PEG8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 59438 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.063 / Rrim(I) all: 0.13 / Χ2: 1.034 / Net I/σ(I): 4.8 / Num. measured all: 231937
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.383.80.46858720.8220.2660.5410.51998
2.38-2.483.60.38258720.8620.2250.4460.55198.3
2.48-2.593.90.31858680.9060.1780.3670.58998.1
2.59-2.7340.25258990.90.1380.2890.68698.5
2.73-2.940.20359070.9550.1120.2330.75598.8
2.9-3.123.80.1659660.9650.090.1850.94898.9
3.12-3.443.90.12259420.9750.0680.1411.26499.2
3.44-3.934.10.10259860.9840.0550.1161.5599.2
3.93-4.953.80.08360050.9880.0470.0961.71998.6
4.95-4040.07261210.9920.040.0831.63698.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J7J

6j7j


Resolution: 2.301→38.041 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 2809 4.85 %
Rwork0.1881 55142 -
obs0.1907 57951 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.28 Å2 / Biso mean: 47.6289 Å2 / Biso min: 16.27 Å2
Refinement stepCycle: final / Resolution: 2.301→38.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8780 0 62 354 9196
Biso mean--36.11 43 -
Num. residues----1111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.301-2.34070.31051130.26052190230376
2.3407-2.38320.30441510.25162690284195
2.3832-2.42910.31321370.24852704284195
2.4291-2.47870.32641220.24232741286394
2.4787-2.53250.27641420.2332745288796
2.5325-2.59140.2971370.22462761289896
2.5914-2.65620.26271360.21582756289296
2.6562-2.7280.2691460.21512788293496
2.728-2.80830.32331560.22022772292897
2.8083-2.89890.25021480.22122737288597
2.8989-3.00250.26791470.22322811295896
3.0025-3.12260.29861420.2142782292496
3.1226-3.26470.26151220.2122796291897
3.2647-3.43670.26971130.20022847296098
3.4367-3.65180.27121340.18322828296297
3.6518-3.93350.21811520.1672832298498
3.9335-4.32890.2031530.15412808296196
4.3289-4.95410.1781390.13772795293496
4.9541-6.23720.21881530.1672856300997
6.2372-38.04630.20271660.16822903306996
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)
13.2820.4293-1.60991.0252-0.9971.55380.2523-0.015-0.12530.1175-0.13650.1066-0.13930.0502-0.11110.46380.04380.03650.3620.07480.4552-67.8485-9.83545.2156
22.0667-0.951-1.3014.92422.28743.52440.28180.307-0.5192-0.1542-0.17680.42730.22-0.0685-0.09010.42260.1316-0.1370.6836-0.05520.6675-77.0147-25.21540.6918
36.7277-2.4107-1.52871.68311.33922.2184-0.07130.3363-0.2464-0.01490.08050.09820.15770.2429-0.0260.32640.0370.00330.3743-0.00210.32675.34376.742415.0122
43.0793-0.3331-0.03232.88060.76746.01740.3573-0.0161-0.3490.1923-0.1001-0.08580.65710.1356-0.21190.42070.0677-0.13840.56020.01020.55116.70070.988729.3637
51.77110.01580.66111.83540.06362.7047-0.0002-0.12150.05010.37820.01930.1025-0.27040.1376-0.01880.40460.0930.01590.24980.01430.3044-46.75835.344533.8555
61.9966-0.7545-0.68111.96740.42532.0454-0.01740.2484-0.1031-0.2125-0.04330.11760.0192-0.09550.06240.3312-0.0037-0.09720.2740.00560.2591-44.8226-6.02928.2472
72.0801-0.9857-2.10351.89330.73842.63680.16740.01420.13820.1192-0.10020.6478-0.8598-0.60990.03540.44990.1410.05180.2695-0.00320.4508-58.212913.612533.3605
81.5098-0.86720.70713.09840.17322.9741-0.04980.1084-0.00450.09090.10790.0038-0.1175-0.1536-0.06170.22210.0010.02050.3002-0.00120.2544-21.46126.749316.0331
91.84360.646-1.44740.6328-0.31082.47060.1261-0.09260.09670.1475-0.0345-0.0209-0.16240.0982-0.08670.3081-0.00760.01250.307-0.00710.2495-19.623328.998639.5117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'M' and (resid 0 through 78 )M0 - 78
2X-RAY DIFFRACTION2chain 'M' and (resid 79 through 187 )M79 - 187
3X-RAY DIFFRACTION3chain 'N' and (resid 0 through 70 )N0 - 70
4X-RAY DIFFRACTION4chain 'N' and (resid 71 through 187 )N71 - 187
5X-RAY DIFFRACTION5chain 'A' and (resid 0 through 154 )A0 - 154
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 364 )A155 - 364
7X-RAY DIFFRACTION7chain 'A' and (resid 365 through 376 )A365 - 376
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 54 )C0 - 54
9X-RAY DIFFRACTION9chain 'C' and (resid 155 through 376 )C155 - 376

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