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- PDB-6j7j: Crystal structure of Pseudomonas aeruginosa Earp -

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Basic information

Entry
Database: PDB / ID: 6j7j
TitleCrystal structure of Pseudomonas aeruginosa Earp
ComponentsPseudomonas aeruginosa Earp
KeywordsTRANSFERASE / rhamnosyltransferase
Function / homologyprotein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Transferases; Glycosyltransferases; Hexosyltransferases / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Pseudomonas aeruginosa Earp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5142
Polymers46,3191
Non-polymers1951
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area16740 Å2
Unit cell
Length a, b, c (Å)45.217, 93.183, 119.886
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M 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 PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 51672 / % possible obs: 98.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.033 / Rrim(I) all: 0.09 / Χ2: 1.447 / Net I/σ(I): 8.7 / Num. measured all: 369193
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.7870.99325480.7910.3971.070.96299.8
1.78-1.817.10.89925060.8090.3590.9690.9896.2
1.81-1.857.10.73925340.8570.2940.7960.968100
1.85-1.897.20.60725350.9030.240.6530.9997.1
1.89-1.937.20.47825400.9460.1890.5140.99299.8
1.93-1.977.20.39625280.9580.1560.4261.0197.5
1.97-2.027.20.33625430.970.1330.3611.014100
2.02-2.077.20.27425630.9770.1090.2951.00498
2.07-2.147.30.2325670.9790.090.2471.02599.9
2.14-2.27.30.18925460.9850.0750.2031.05598.6
2.2-2.287.30.15525710.9910.0610.1671.11798.8
2.28-2.387.30.13125840.9930.0520.1411.1699.7
2.38-2.487.40.1225740.9950.0470.1291.26999.4
2.48-2.617.30.10625890.9960.0420.1141.48399.3
2.61-2.787.20.09426070.9960.0370.1011.81199.5
2.78-2.997.10.08326370.9940.0330.0892.04499.6
2.99-3.297.10.06826120.9970.0280.0742.21999.6
3.29-3.776.80.05326600.9970.0220.0582.27599.8
3.77-4.757.10.04726710.9980.0190.0512.51199.7
4.75-406.50.0527570.9970.0210.0553.07396.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→38.523 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 2608 5.07 %
Rwork0.1752 48801 -
obs0.1769 51409 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.11 Å2 / Biso mean: 35.3643 Å2 / Biso min: 14.23 Å2
Refinement stepCycle: final / Resolution: 1.75→38.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 12 352 3368
Biso mean--35.87 45.08 -
Num. residues----377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.78190.32031510.277125262677100
1.7819-1.81610.29011370.2542476261397
1.8161-1.85320.28551310.234625632694100
1.8532-1.89350.25261260.22072479260597
1.8935-1.93750.2841330.203125502683100
1.9375-1.9860.22061430.18932491263498
1.986-2.03970.20841390.187625582697100
2.0397-2.09970.27641240.18562539266399
2.0997-2.16750.25321450.17762557270299
2.1675-2.24490.19051490.173425302679100
2.2449-2.33480.2011230.16782574269799
2.3348-2.4410.21731100.17332586269699
2.441-2.56970.21861380.18562563270199
2.5697-2.73070.2041510.173325852736100
2.7307-2.94140.20531300.18226002730100
2.9414-3.23730.22031360.178426492785100
3.2373-3.70540.20671510.162626072758100
3.7054-4.66720.1731460.142226522798100
4.6672-38.53240.18851450.17652716286197
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)
11.3013-0.4283-0.45531.61130.15384.17510.0012-0.18830.15770.15930.0375-0.0108-0.25540.0383-0.02740.1822-0.02660.00790.21570.00990.212939.626-8.4854120.4363
20.7706-0.28440.43233.0842-1.21242.2383-0.00420.05040.062-0.2169-0.0474-0.1853-0.05280.00970.04080.1797-0.01440.00330.17660.01660.162239.89461.424992.2962
33.1013-0.102-0.18725.5896-3.19937.35030.0428-0.1448-0.49490.11340.11560.24360.56270.0065-0.13110.2207-0.03550.010.24630.02590.286835.9221-25.067121.1778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 154 )A-2 - 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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