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- PDB-5f9z: Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium ... -

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Basic information

Entry
Database: PDB / ID: 5f9z
TitleCrystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with Halofuginone and AMPPNP
ComponentsAminoacyl-tRNA synthetaseAminoacyl tRNA synthetase
KeywordsLIGASE / SSGCID / prolyl-tRNA ligase / Cryptosporidium parvum / ATP binding / aminoacylation / halofuginone / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / proline--tRNA ligase / Proline--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.4 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 Halofuginone and AMPPNP
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 1.1Sep 27, 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 / pdbx_struct_oper_list / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)120,73711
Polymers118,6242
Non-polymers2,1139
Water7,855436
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A: Aminoacyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3235
Polymers59,3121
Non-polymers1,0114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminoacyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4156
Polymers59,3121
Non-polymers1,1035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-46 kcal/mol
Surface area37280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.400, 108.720, 126.350
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 / 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 , 6 types, 445 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone / Halofuginone


Mass: 414.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
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 4 mM MgCl2, halofuginone, and AMPPNP, then mixed 1:1 with Top96(a5):0.1 M HEPES:NaOH, pH = 7.5, 20% (w/v) PEG-4000, 10% (v/v) ...Details: CrpaA.18681.a.B3.PW37711 at 21.5 mg/mlprotein was incubated with 4 mM MgCl2, halofuginone, and AMPPNP, then mixed 1:1 with Top96(a5):0.1 M HEPES:NaOH, pH = 7.5, 20% (w/v) PEG-4000, 10% (v/v) 2-propanol, harvested with 20% ethylene glycol4 mM MgCl2, halofuginone, and AMPPNP, then mixed 1:1 with Top96(a5):0.1 M HEPES:NaOH, pH = 7.5, 20% (w/v) PEG-4000, 10% (v/v) 2-propanol, harvested with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 9, 2015
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 48156 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 31.54 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.119 / Χ2: 0.97 / Net I/σ(I): 11.07 / Num. measured all: 205387
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.463.70.8370.5732.612774358134200.66295.5
2.46-2.530.8540.4883.112766350533690.56296.1
2.53-2.60.890.4383.3912697335732710.50397.4
2.6-2.680.9120.3713.9412667328532300.42798.3
2.68-2.770.9360.3114.6712799319031610.35699.1
2.77-2.870.9560.2645.3212856312530970.30199.1
2.87-2.980.9650.2226.2112517296829480.25399.3
2.98-3.10.9720.1937.2512534288328560.21999.1
3.1-3.240.9830.1539.3512169273727130.17399.1
3.24-3.390.9890.12711.5512062266426310.14398.8
3.39-3.580.9920.10314.6911309252224860.11798.6
3.58-3.790.9930.08318.2510624239423570.09498.5
3.79-4.060.9950.07918.3510075226322390.0998.9
4.06-4.380.9960.06621.129332210920930.07599.2
4.38-4.80.9970.05624.198574193619120.06398.8
4.8-5.370.9970.05922.588199177817660.06799.3
5.37-6.20.9960.06719.317437157915700.07599.4
6.2-7.590.9970.05621.056386135213490.06399.8
7.59-10.730.9990.03129.934972107010690.03599.9
10.73-500.9990.02536.326386496190.02995.4

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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
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5F9Y

5f9y


Resolution: 2.4→46.611 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 2063 4.29 %
Rwork0.2075 46026 -
obs0.2087 48089 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.41 Å2 / Biso mean: 37.0439 Å2 / Biso min: 15.46 Å2
Refinement stepCycle: final / Resolution: 2.4→46.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7719 0 120 436 8275
Biso mean--33.15 36.97 -
Num. residues----981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028065
X-RAY DIFFRACTIONf_angle_d0.48610968
X-RAY DIFFRACTIONf_chiral_restr0.0441214
X-RAY DIFFRACTIONf_plane_restr0.0031384
X-RAY DIFFRACTIONf_dihedral_angle_d14.0554793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.45580.30751350.27862947308295
2.4558-2.51720.29411340.25052958309296
2.5172-2.58520.24531450.25682952309797
2.5852-2.66130.28531310.24833041317298
2.6613-2.74720.27971270.24063060318799
2.7472-2.84540.25031350.24993040317599
2.8454-2.95930.29471410.2443076321799
2.9593-3.09390.28291300.2463094322499
3.0939-3.2570.27621410.22763062320399
3.257-3.4610.22241150.21573064317998
3.461-3.72810.2321440.19853075321999
3.7281-4.10310.21051320.18563109324199
4.1031-4.69640.18291410.16223121326299
4.6964-5.9150.19731500.16563142329299
5.915-46.61980.20781620.18753285344799
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)
13.47320.89081.823.9424-1.5062.5110.0833-0.37360.38630.6319-0.0627-0.2604-0.4348-0.14870.00110.2214-0.02610.0080.2997-0.04060.305628.448623.891536.8933
21.2131-0.48450.0291.00010.82511.61570.04920.21130.1588-0.18050.0697-0.0592-0.1472-0.0072-0.11650.2382-0.0210.04080.1870.03440.169715.415712.040815.7209
30.8835-0.29270.0011.3220.17541.43770.00840.20650.127-0.2861-0.0002-0.0691-0.10950.0997-0.01570.2464-0.02140.03650.21160.04670.175314.447119.21089.7887
40.95960.2974-0.68962.1042-1.55342.88170.0016-0.1050.10530.03310.0961-0.1567-0.1874-0.0191-0.07960.18240.0056-0.01620.1918-0.06870.231313.922128.482535.4517
51.5806-0.36770.62241.7099-0.08721.80720.13660.2833-0.1513-0.3548-0.05840.05630.0175-0.0214-0.0760.16180.0110.01960.1835-0.02630.212111.0632-6.308210.64
62.8838-0.0591-0.18842.4122-0.03283.78010.07690.1248-0.0718-0.11020.057-0.5580.28290.7491-0.08640.26140.04130.01670.4312-0.03650.404235.61542.483420.0428
71.26230.10850.53051.0254-0.07181.10740.03410.0651-0.058-0.05350.07420.00960.03990.073-0.10850.20090.03560.03190.17790.01010.139811.7851-6.869420.7523
82.7811-1.33590.45622.0953-0.18920.7710.19970.0594-0.6436-0.14980.0067-0.14330.38340.1912-0.20320.38970.0921-0.07560.2681-0.0430.444919.8382-29.615621.7913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 179 through 229 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 230 through 279 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 464 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 465 through 688 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 191 through 250 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 251 through 287 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 288 through 574 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 575 through 688 )B0

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