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- PDB-6j7k: Crystal structure of Pseudomonas aeruginosa Earp in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6j7k
TitleCrystal structure of Pseudomonas aeruginosa Earp in complex with TDP-Rha
ComponentsPseudomonas aeruginosa Earp
KeywordsTRANSFERASE / rhamnosyltransferase
Function / homologyprotein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Transferases; Glycosyltransferases; Hexosyltransferases / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudomonas aeruginosa Earp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0623
Polymers46,3191
Non-polymers7442
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-7 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.521, 92.366, 119.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pseudomonas aeruginosa Earp


Mass: 46318.742 Da / Num. of mol.: 1
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: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH6.5, 12% PEG20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 28155 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Χ2: 0.614 / Net I/σ(I): 4.9 / Num. measured all: 186832
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.196.90.56913970.8620.2280.6150.46198.9
2.19-2.236.80.72413660.8550.2930.7820.48699.4
2.23-2.273.70.32411970.9020.1870.3771.91284.1
2.27-2.3260.66713450.8970.2860.7280.54698
2.32-2.376.30.33814100.9450.1420.3680.47799.3
2.37-2.426.70.30513960.9450.1250.3310.46499.4
2.42-2.486.50.25813810.9680.1070.280.46799.5
2.48-2.557.10.23614230.9750.0920.2540.49599.6
2.55-2.627.20.19213800.9830.0750.2070.48799.6
2.62-2.717.10.19714220.9760.0780.2120.65399.9
2.71-2.817.10.14114120.9920.0560.1520.50599.9
2.81-2.927.20.1214060.9930.0470.1290.49799.6
2.92-3.057.10.10314280.9940.0410.1110.51899.9
3.05-3.216.90.07914120.9960.0320.0850.52100
3.21-3.416.60.0714200.9960.030.0760.607100
3.41-3.6860.08214230.9910.0370.0911.00399
3.68-4.056.30.07714300.990.0340.0851.23699.2
4.05-4.637.40.04214560.9990.0160.0450.601100
4.63-5.836.80.0414810.9990.0160.0430.55199.6
5.83-406.50.04215700.9990.0170.0450.67299.8

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Processing

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

6j7j


Resolution: 2.15→38.638 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1350 4.87 %
Rwork0.2168 26389 -
obs0.2188 27739 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.46 Å2 / Biso mean: 35.6682 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: final / Resolution: 2.15→38.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 47 220 3365
Biso mean--30.42 36.85 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1501-2.22690.36071250.31562595272099
2.2269-2.3160.49950.44792374246988
2.316-2.42140.3031380.24332620275899
2.4214-2.54910.25361380.239826242762100
2.5491-2.70870.28751380.226426452783100
2.7087-2.91780.28991460.228526352781100
2.9178-3.21130.28361450.226326772822100
3.2113-3.67570.22121440.20692665280999
3.6757-4.62980.22611460.164627132859100
4.6298-38.64420.20051350.16972841297699
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)
11.38950.20410.49391.96680.36413.87350.12130.1493-0.2729-0.12730.03640.01070.3173-0.0097-0.13520.15610.0098-0.03860.22860.02250.249240.621454.04740.1085
21.275-0.0531-0.00453.4641-1.55762.53910.026-0.0952-0.05360.264-0.0583-0.11320.00710.1510.00160.2001-0.0077-0.01460.2190.01430.161740.567545.30427.5211
36.02870.073-0.63836.5602-3.0477.65240.17720.19530.5374-0.1093-0.04170.0115-0.39950.1797-0.22070.15850.0109-0.00960.2022-0.00180.243936.516171.1803-1.4554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 154 )A0 - 154
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 363 )A155 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 384 )A364 - 384

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