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- PDB-5ucm: Crystal Structure of Prolyl-tRNA Synthetase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 5ucm
TitleCrystal Structure of Prolyl-tRNA Synthetase from Pseudomonas aeruginosa
ComponentsProline--tRNA ligase
KeywordsLIGASE / SSGCID / ProRS / Proline-tRNA ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytosol
Similarity search - Function
Prolyl-tRNA synthetase, class IIa, type 1 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / Anticodon-binding domain / : ...Prolyl-tRNA synthetase, class IIa, type 1 / Prolyl-tRNA synthetase, class IIa, bacterial-type / Prokaryote proline-tRNA ligase core domain / Proline--tRNA ligase, anticodon binding domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / Anticodon-binding domain / : / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proline--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Protein Sci. / Year: 2019
Title: Characterization and structure determination of prolyl-tRNA synthetase from Pseudomonas aeruginosa and development as a screening platform.
Authors: Pena, N. / Dranow, D.M. / Hu, Y. / Escamilla, Y. / Bullard, J.M.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 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 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4664
Polymers128,4182
Non-polymers492
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-34 kcal/mol
Surface area45120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.830, 101.540, 187.240
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 Proline--tRNA ligase / Prolyl-tRNA synthetase / ProRS


Mass: 64208.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: proS, PA0956 / Plasmid: PsaeA.17981.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I502, proline-tRNA ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PsaeA.17981.a.B1.PW37621 at 9.5 mg/ml, incubated with 1 mM proline, AMPPNP, MgCl2 and mixed 1:1 with an equal volume MCSG1(b11): 20% (w/v) PEG-8000, 0.2 M MgCl2, 0.1 M Tris:HCl, pH=8.5, ...Details: PsaeA.17981.a.B1.PW37621 at 9.5 mg/ml, incubated with 1 mM proline, AMPPNP, MgCl2 and mixed 1:1 with an equal volume MCSG1(b11): 20% (w/v) PEG-8000, 0.2 M MgCl2, 0.1 M Tris:HCl, pH=8.5, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→49.001 Å / Num. obs: 49894 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.459 % / Biso Wilson estimate: 28.32 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.148 / Χ2: 0.941 / Net I/σ(I): 9.75 / Num. measured all: 222455 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.674.4470.5852.6716495374237090.6890.66699.1
2.67-2.744.4650.4833.1515934361035690.7880.54998.9
2.74-2.824.4650.4433.4715604354434950.8030.50498.6
2.82-2.914.4650.3554.1815166344033970.8540.40398.8
2.91-34.4570.2934.9914625332532810.90.33398.7
3-3.114.4730.2455.8814331325332040.9310.27898.5
3.11-3.224.4880.2146.6113707310530540.9490.24298.4
3.22-3.364.4620.1728.0413097299029350.9650.19498.2
3.36-3.514.4710.1399.8212775293228570.9740.15797.4
3.51-3.684.4950.11611.3812127275726980.9840.13197.9
3.68-3.884.4850.09713.0811494262625630.990.10997.6
3.88-4.114.4860.08314.8410956252124420.9910.09496.9
4.11-4.394.4710.07316.4710186235222780.9930.08296.9
4.39-4.754.460.06717.799540221121390.9930.07696.7
4.75-5.24.5030.06418.268768202419470.9950.07296.2
5.2-5.814.4680.07216.497927185917740.9930.08195.4
5.81-6.714.4520.07216.417030166315790.9930.08294.9
6.71-8.224.4120.06119.055907140913390.9940.06995
8.22-11.634.3190.0524.314496112010410.9960.05692.9
11.63-49.0013.8620.04624.2922906725930.9960.05388.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J3L

2j3l


Resolution: 2.6→49.001 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.9
RfactorNum. reflection% reflection
Rfree0.2324 1877 3.97 %
Rwork0.1686 --
obs0.1712 47231 92.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.54 Å2 / Biso mean: 35.6269 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.6→49.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8599 0 2 488 9089
Biso mean--48.6 31.71 -
Num. residues----1129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078814
X-RAY DIFFRACTIONf_angle_d0.88411970
X-RAY DIFFRACTIONf_chiral_restr0.051352
X-RAY DIFFRACTIONf_plane_restr0.0061579
X-RAY DIFFRACTIONf_dihedral_angle_d15.0885342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.67030.32251330.2293211334486
2.6703-2.74890.30981340.21813231336587
2.7489-2.83760.31451290.21363320344989
2.8376-2.9390.23311420.23361350390
2.939-3.05660.28791450.23467361293
3.0566-3.19570.30831430.19183425356892
3.1957-3.36420.27421470.19893542368994
3.3642-3.57490.24831520.1783591374395
3.5749-3.85080.22651480.15583585373396
3.8508-4.23810.19851480.13433605375395
4.2381-4.85090.17231530.123654380796
4.8509-6.10980.17981460.14163640378695
6.1098-49.00930.19261570.16533722387993
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)
11.9840.42970.18792.2050.37872.04630.1528-0.2855-0.17960.2599-0.0179-0.17820.20410.3148-0.07090.2254-0.0024-0.08630.2773-0.00880.196642.213743.499980.7658
21.2565-0.1229-0.30151.53650.83451.20010.04650.09420.1794-0.1426-0.05880.0429-0.2003-0.08580.02340.19410.0414-0.0090.19790.04290.192729.469356.568160.5715
32.1212-0.5777-0.67620.23830.34220.5215-0.03960.05770.10360.0834-0.004-0.0176-0.11490.15370.02810.20710.0081-0.03570.24930.0130.29140.418856.37469.227
42.36540.5552-0.47022.7683-0.90861.54280.1851-0.39970.41320.3867-0.11280.1411-0.22910.0119-0.03850.3292-0.0158-0.00150.24-0.11940.2436.147168.643579.8415
51.31030.3902-0.50341.2752-0.38951.63590.2021-0.26070.22380.2983-0.2016-0.0911-0.31990.4585-0.00250.2866-0.0771-0.04070.3223-0.0550.271761.244683.323266.8452
62.9806-0.02252.20440.25910.09612.34370.05010.15190.4507-0.054-0.11570.1353-0.18730.05180.09760.34770.01650.00920.16690.05950.378930.707970.566367.2332
71.4485-0.258-0.16072.9974-1.00261.34530.3117-0.3955-0.06330.2022-0.211-0.20760.43980.2422-0.06330.363-0.0347-0.11480.4468-0.00330.242642.06248.209387.6289
81.4418-0.15150.46790.8843-1.47243.08620.4592-0.307-0.31870.2702-0.09950.16330.5869-0.3684-0.3140.626-0.1544-0.17220.54770.07910.342341.69735.839102.7576
93.91890.022-0.80984.2374-0.24611.3752-0.13170.01580.2721-0.12220.10.2509-0.1997-0.21770.07710.17920.0561-0.04490.27870.06660.209614.366450.61163.0452
100.48240.65920.00011.156-0.17970.66460.0095-0.0783-0.13350.0195-0.0545-0.16950.14790.02940.03470.18230.0506-0.02410.23370.0130.207430.797931.639568.4218
110.5253-0.12750.00370.60390.39622.17220.04920.0075-0.13560.1048-0.07410.04120.2288-0.16720.03730.1769-0.04730.00140.1770.0310.225315.50337.356444.8177
120.56630.41510.01670.6597-0.11930.9233-0.02330.0145-0.23240.0971-0.02650.02020.2135-0.02680.02580.23750.0201-0.01980.1986-0.01360.192825.236327.292168.8767
131.3255-0.2311-0.13930.72210.02721.4576-0.3683-0.77270.18160.61140.23330.427-0.1385-0.29040.06560.36880.13670.07760.6143-0.0760.37480.493455.040381.3689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 63 )A2 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 139 )A64 - 139
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 166 )A140 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 213 )A167 - 213
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 400 )A214 - 400
6X-RAY DIFFRACTION6chain 'A' and (resid 401 through 437 )A401 - 437
7X-RAY DIFFRACTION7chain 'A' and (resid 438 through 483 )A438 - 483
8X-RAY DIFFRACTION8chain 'A' and (resid 484 through 570 )A484 - 570
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 43 )B1 - 43
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 213 )B44 - 213
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 400 )B214 - 400
12X-RAY DIFFRACTION12chain 'B' and (resid 401 through 466 )B401 - 466
13X-RAY DIFFRACTION13chain 'B' and (resid 467 through 570 )B467 - 570

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