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- PDB-6nab: Crystal structure of prolyl-tRNA synthetase from Naegleria fowler... -

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Basic information

Entry
Database: PDB / ID: 6nab
TitleCrystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)
ComponentsProlyl-tRNA synthetase
KeywordsLIGASE / SSGCID / 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 / ATP binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / 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) ...C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / 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 / PROLINE / Proline--tRNA ligase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl-tRNA synthetase
B: Prolyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,85521
Polymers119,0752
Non-polymers1,78019
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint6 kcal/mol
Surface area37770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.930, 66.100, 112.980
Angle α, β, γ (deg.)90.000, 102.030, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 6 or resid 8...
21(chain B and (resid 4 through 6 or resid 8...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUILEILE(chain A and (resid 4 through 6 or resid 8...AA4 - 612 - 14
12VALVALVALVAL(chain A and (resid 4 through 6 or resid 8...AA8 - 5016 - 58
13LYSLYSPHEPHE(chain A and (resid 4 through 6 or resid 8...AA52 - 5460 - 62
14ASNASNASNASN(chain A and (resid 4 through 6 or resid 8...AA99107
15GLUGLUTYRTYR(chain A and (resid 4 through 6 or resid 8...AA4 - 50512 - 513
16GLUGLUTYRTYR(chain A and (resid 4 through 6 or resid 8...AA4 - 50512 - 513
17GLUGLUTYRTYR(chain A and (resid 4 through 6 or resid 8...AA4 - 50512 - 513
18GLUGLUTYRTYR(chain A and (resid 4 through 6 or resid 8...AA4 - 50512 - 513
19GLUGLUTYRTYR(chain A and (resid 4 through 6 or resid 8...AA4 - 50512 - 513
21GLUGLUILEILE(chain B and (resid 4 through 6 or resid 8...BB4 - 612 - 14
22VALVALVALVAL(chain B and (resid 4 through 6 or resid 8...BB8 - 5016 - 58
23LYSLYSLYSLYS(chain B and (resid 4 through 6 or resid 8...BB5260
24GLUGLUTYRTYR(chain B and (resid 4 through 6 or resid 8...BB4 - 50512 - 513
25GLUGLUTYRTYR(chain B and (resid 4 through 6 or resid 8...BB4 - 50512 - 513
26GLUGLUTYRTYR(chain B and (resid 4 through 6 or resid 8...BB4 - 50512 - 513
27GLUGLUTYRTYR(chain B and (resid 4 through 6 or resid 8...BB4 - 50512 - 513

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prolyl-tRNA synthetase


Mass: 59537.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Plasmid: NafoA.18681.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A4V8H034*PLUS

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Non-polymers , 5 types, 811 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Anatrace TOP86 screen, condition D7: 200mM Ammonium sulfate, 30% PEG 8000: NAFOA.18681.a.B2.PW37988 at 22.6mg/ml + 5mM CaCl2: cryo 15% EG: tray 287001 d7: puck XFD3-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→38.372 Å / Num. obs: 76263 / % possible obs: 99.4 % / Redundancy: 3.671 % / Biso Wilson estimate: 29.581 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.094 / Χ2: 0.992 / Net I/σ(I): 12.78 / Num. measured all: 279947 / Scaling rejects: 2
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
2-2.052.8230.4952.2415053565253330.7390.60694.4
2.05-2.113.1870.4153.0517404546754610.8220.49799.9
2.11-2.173.5780.3623.8319209537453680.8790.42699.9
2.17-2.243.8140.2964.9219760518951810.9330.34599.8
2.24-2.313.8160.2575.7419225504850380.9460.29999.8
2.31-2.393.8190.2226.4718436482848270.9580.258100
2.39-2.483.8270.1867.5918192476447540.970.21699.8
2.48-2.583.8220.1519.0417277452745200.9780.17699.8
2.58-2.73.8230.13210.1616553432943300.9830.154100
2.7-2.833.8260.11111.9515962418541720.9870.1399.7
2.83-2.983.8250.09214.1715140396439580.9910.10799.8
2.98-3.163.8130.07316.8214371378237690.9930.08699.7
3.16-3.383.8120.05820.3313328349434960.9960.068100
3.38-3.653.7970.04524.5712487330232890.9970.05399.6
3.65-43.780.03927.9311394302430140.9980.04599.7
4-4.473.7580.03531.2210328276127480.9980.04199.5
4.47-5.163.7550.03233.279103243224240.9980.03899.7
5.16-6.323.7490.03430.777768208120720.9980.0499.6
6.32-8.943.6710.03331.735906161716090.9980.03999.5
8.94-38.3723.390.03135.6830519329000.9980.03696.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3339)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
SIMBADphasing
PHASERphasing
ARP/wARPmodel building
Cootmodel building
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4hvcAB as per MoRDa

Resolution: 2→38.372 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 1991 2.61 %0
Rwork0.1512 74262 --
obs0.1522 76253 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.63 Å2 / Biso mean: 29.5298 Å2 / Biso min: 9.14 Å2
Refinement stepCycle: final / Resolution: 2→38.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7919 0 116 802 8837
Biso mean--30.47 37.01 -
Num. residues----993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078347
X-RAY DIFFRACTIONf_angle_d0.84311336
X-RAY DIFFRACTIONf_dihedral_angle_d13.3634991
X-RAY DIFFRACTIONf_chiral_restr0.0541225
X-RAY DIFFRACTIONf_plane_restr0.0061473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4532X-RAY DIFFRACTION4.638TORSIONAL
12B4532X-RAY DIFFRACTION4.638TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.26531430.22674973511694
2.05-2.10540.23811340.191853015435100
2.1054-2.16740.24821430.181952785421100
2.1674-2.23730.18991320.167453325464100
2.2373-2.31730.21551420.161252825424100
2.3173-2.41010.21851370.159453315468100
2.4101-2.51970.21181380.159553295467100
2.5197-2.65250.23321370.153653215458100
2.6525-2.81870.21111380.161453185456100
2.8187-3.03620.22431490.155653185467100
3.0362-3.34160.19591450.150453265471100
3.3416-3.82480.15941460.131353415487100
3.8248-4.81740.13851530.116853495502100
4.8174-38.37870.17451540.15255463561799
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)
11.478-0.0674-0.30370.55120.08391.45660.00380.02980.2083-0.0129-0.0369-0.0145-0.0983-0.11150.01740.1336-0.0145-0.0270.0788-0.01440.158257.87610.46121.691
20.7080.02250.00760.637-0.04260.85310.0128-0.08660.05610.0111-0.0239-0.08990.04330.0245-0.00360.14970.0037-0.02910.1141-0.02060.162869.9069.41130.629
32.00761.99952.01142.0092.01222.03240.4239-1.3081.58080.4771-0.56830.5637-0.5704-0.02640.14460.16680.0201-0.02260.2608-0.04680.248956.44616.26533.66
41.51110.4231-0.1511.21370.13521.17140.02670.05650.0951-0.042-0.0660.0373-0.0319-0.15810.03930.0981-0.014-0.02140.1601-0.01230.124142.8640.35718.486
51.36530.21260.17931.16060.16541.46030.0123-0.161-0.0740.1517-0.0636-0.03140.1145-0.13920.05960.133-0.0388-0.00680.1634-0.02280.146640.441-9.32725.692
60.82950.16470.36930.87040.58241.09480.0836-0.3549-0.06370.2051-0.18310.14270.1477-0.28690.09270.2114-0.10120.03590.3029-0.01280.196325.512-14.24425.829
75.25231.1294-0.20768.57333.51732.1356-0.92931.8225-0.1643-0.56740.56120.17730.0350.1050.38380.1721-0.04890.08610.10080.03230.163341.87-2.02811.796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:105 )A4 - 105
2X-RAY DIFFRACTION2( CHAIN A AND RESID 106:505 )A106 - 505
3X-RAY DIFFRACTION3( CHAIN A AND RESID 602:602 )A602
4X-RAY DIFFRACTION4( CHAIN B AND RESID 4:189 )B4 - 189
5X-RAY DIFFRACTION5( CHAIN B AND RESID 190:334 )B190 - 334
6X-RAY DIFFRACTION6( CHAIN B AND RESID 335:505 )B335 - 505
7X-RAY DIFFRACTION7( CHAIN B AND RESID 602:602 )B602

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