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- PDB-5f9y: Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium ... -

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Basic information

Entry
Database: PDB / ID: 5f9y
TitleCrystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Proline and AMP
ComponentsAminoacyl-tRNA synthetase
KeywordsLIGASE / SSGCID / prolyl-tRNA ligase / Cryptosporidium parvum / ATP binding / aminoacylation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / ProRS
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type ...C-terminal domain of ProRS / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / 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
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / PROLINE / proline--tRNA ligase / Proline--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Proline and AMP
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Dranow, D.M. / Fox III, D. / Lorimer, D. / Edwards, T.E.
History
DepositionDec 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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: Aminoacyl-tRNA synthetase
B: Aminoacyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7759
Polymers118,6242
Non-polymers1,1507
Water63135
1
A: Aminoacyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8404
Polymers59,3121
Non-polymers5283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminoacyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9355
Polymers59,3121
Non-polymers6234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-71 kcal/mol
Surface area36400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.870, 110.140, 127.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aminoacyl-tRNA synthetase


Mass: 59312.008 Da / Num. of mol.: 2 / Fragment: UNP residues 186-688
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: 1MB.635 / Plasmid: CrpaA.18681.a.B3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7YZ69, UniProt: A0A7G2HJF2*PLUS

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Non-polymers , 5 types, 42 molecules

#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: CrpaA.18681.a.B3.PW37711 at 21.5 mg/mlprotein was incubated with 3 mM MgCl2, L-proline, and AMPPNP, then mixed 1:1 with Morpheus(c5): 10% (w/v) PEG-20,000, 20% (w/v) PEG MME 550, 0.1 M MOPS/ ...Details: CrpaA.18681.a.B3.PW37711 at 21.5 mg/mlprotein was incubated with 3 mM MgCl2, L-proline, and AMPPNP, then mixed 1:1 with Morpheus(c5): 10% (w/v) PEG-20,000, 20% (w/v) PEG MME 550, 0.1 M MOPS/ HEPES-Na, pH = 7.5, 0.03 M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate

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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 225 mm CCD / Detector: CCD / Date: Jul 30, 2015 / 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: 2.8→50 Å / Num. obs: 32278 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 47.65 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.091 / Χ2: 0.951 / Net I/σ(I): 19.67 / Num. measured all: 199297
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.870.8470.5823.5214621233323330.635100
2.87-2.950.9020.4844.214522231723170.528100
2.95-3.040.9320.3665.5313993223422320.499.9
3.04-3.130.9560.2986.6813552216421630.325100
3.13-3.230.9750.2228.7613194210421030.243100
3.23-3.350.9860.16911.1312662202620260.185100
3.35-3.470.990.1313.9512328197419740.142100
3.47-3.610.9940.10716.3711846189418930.11699.9
3.61-3.780.9960.08520.1611321182718260.09399.9
3.78-3.960.9970.07322.5810916175117500.07999.9
3.96-4.170.9980.06425.2910306166116610.07100
4.17-4.430.9980.0530.459826159215920.054100
4.43-4.730.9990.04135.439136148114800.04599.9
4.73-5.110.9990.03936.68522139513950.043100
5.11-5.60.9980.04533.797837128412840.049100
5.6-6.260.9980.04632.887088117411720.05199.8
6.26-7.230.9980.04135.956228104510450.045100
7.23-8.850.9990.0344.5353229059050.033100
8.85-12.520.9990.02354.7340307107090.02699.9
12.52-500.9990.02352.1820474394180.02695.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2219refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HVC

4hvc


Resolution: 2.8→46.611 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1881 6.1 %
Rwork0.2137 28958 -
obs0.2156 30839 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.9 Å2 / Biso mean: 50.6131 Å2 / Biso min: 16.65 Å2
Refinement stepCycle: final / Resolution: 2.8→46.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 0 69 35 7436
Biso mean--88.28 35.01 -
Num. residues----955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027605
X-RAY DIFFRACTIONf_angle_d0.51110356
X-RAY DIFFRACTIONf_chiral_restr0.0441166
X-RAY DIFFRACTIONf_plane_restr0.0041313
X-RAY DIFFRACTIONf_dihedral_angle_d12.1494521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.87570.32511250.30912002212788
2.8757-2.96030.33211620.28962058222090
2.9603-3.05590.33751280.26282102223092
3.0559-3.16510.30771250.26372152227793
3.1651-3.29180.30321390.25182182232195
3.2918-3.44150.29881440.24242223236796
3.4415-3.62290.24251560.21832238239498
3.6229-3.84980.23851330.20992287242098
3.8498-4.14690.23811650.19642260242598
4.1469-4.56390.1871440.172316246099
4.5639-5.22360.19391510.16452311246299
5.2236-6.57830.23691510.20612363251499
6.5783-47.1030.21341580.21072464262299
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)
11.6668-0.5840.56592.0706-0.06623.15890.091-0.22110.30170.22480.125-0.5606-0.14840.3372-0.1510.2056-0.02320.03080.3099-0.06860.370322.718120.66233.5995
23.5335-0.6523-1.06341.7213-0.03462.78810.09050.56490.1812-0.47320.0203-0.43820.13220.2454-0.1610.3754-0.01110.13750.43860.00970.342225.29618.46356.1727
31.2444-0.71830.30851.92130.49954.26330.15140.00920.0503-0.35920.0831-0.2208-0.13-0.0832-0.17720.3399-0.00260.0990.19920.03420.230715.397413.78659.6256
43.02590.2661.15573.3009-0.70373.5536-0.14380.33840.5027-0.4160.2302-0.2098-0.67390.1324-0.19730.3309-0.05320.04040.22910.02420.27148.715126.711414.0332
51.0832-0.09060.0761.2690.39621.8949-0.1182-0.11380.0573-0.01670.1186-0.21160.02240.2120.04960.15560.0283-0.00020.1665-0.01590.272914.610318.872132.0841
61.42390.1285-0.3892.8747-0.93422.5010.1107-0.17560.42530.04690.1096-0.2325-0.60030.2179-0.13730.3046-0.0538-0.00090.2258-0.03810.406312.491933.9934.4157
71.57791.05390.73094.00480.59342.0273-0.03190.12270.8724-0.2550.44070.0585-0.4282-0.2414-0.28470.5837-0.07590.17810.43580.23050.653115.367343.957812.4744
88.4689-1.6372-4.296920.97719.4504-0.59781.61640.6987-3.27711.0212-0.5912-1.3597-1.0073-0.37050.4347-0.02280.16251.05520.19950.410116.847719.602810.0562
92.1116-0.98690.33992.0497-0.66621.77940.10830.3934-0.2959-0.5327-0.08750.0575-0.26770.18750.01320.2005-0.0040.03820.2033-0.06110.24710.8848-6.184911.2207
102.8015-0.0304-0.4552.3214-0.59195.5617-0.064-0.14750.27220.00650.1549-0.68560.16720.7750.11460.19470.03080.03170.3541-0.02610.426633.42365.165523.3849
111.29420.93721.12922.40350.46572.07950.1514-0.1251-0.21320.3225-0.0472-0.28920.41170.3135-0.09890.2530.1065-0.00240.2929-0.05240.306122.634-10.295326.7493
121.85050.24530.53791.89730.34521.05330.05270.0241-0.41930.06580.118-0.20530.18790.226-0.20250.25950.09060.04610.22590.04260.188314.5002-6.872523.1751
132.3027-0.63280.68461.52671.00831.36660.15240.42480.6353-0.4640.33890.314-0.7008-0.1980.28030.4350.09-0.06120.34840.20760.4215-11.0471-1.68848.2525
144.1729-1.16550.14582.952-0.42311.90740.1896-0.0274-0.6412-0.20020.0939-0.04240.47120.2177-0.19580.43660.013-0.0710.207-0.07220.27658.6634-23.279419.1877
1521.9999-6.032.0001-0.23757.91460.3008-1.0237-0.72812.25410.5741-2.62870.93550.4625-1.01390.6927-0.1293-0.16260.54890.01070.317727.3316-6.62425.2925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 179 through 250 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 251 through 301 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 302 through 357 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 358 through 399 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 400 through 542 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 543 through 633 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 634 through 688 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 700 through 700 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 191 through 250 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 251 through 312 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 313 through 424 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 425 through 493 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 494 through 534 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 535 through 688 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 700 through 700 )B0

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