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- PDB-6blj: Crystal structure of cytoplasmic Serine-tRNA ligase from Naegleri... -

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Basic information

Entry
Database: PDB / ID: 6blj
TitleCrystal structure of cytoplasmic Serine-tRNA ligase from Naegleria fowleri in complex with AMP
ComponentsSerine-tRNA ligase
KeywordsLIGASE / SSGCID / Structural Genomics / Naegleria fowleri / cystsolic serine--trna ligase / Adenosine monophosphate / Seattle Structural Genomics Center for Infectious Disease
Function / homologyBira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 2-Layer Sandwich / Alpha Beta / ADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of cytoplasmic Serine-tRNA ligase from Neisseria fowlerii in complex with AMP
Authors: Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2018Group: Atomic model / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy
Revision 2.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine-tRNA ligase
B: Serine-tRNA ligase
C: Serine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,1369
Polymers165,9093
Non-polymers1,2286
Water18,3571019
1
A: Serine-tRNA ligase
B: Serine-tRNA ligase
C: Serine-tRNA ligase
hetero molecules

B: Serine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,84912
Polymers221,2124
Non-polymers1,6378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2
A: Serine-tRNA ligase
C: Serine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4246
Polymers110,6062
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-25 kcal/mol
Surface area37140 Å2
MethodPISA
3
B: Serine-tRNA ligase
hetero molecules

B: Serine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4246
Polymers110,6062
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6300 Å2
ΔGint-26 kcal/mol
Surface area35990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.190, 168.190, 111.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-658-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -2 through 9 or (resid 10...
21(chain B and (resid -2 through 9 or (resid 10...
31(chain C and (resid -2 through 19 or resid 21...

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
11HISHISGLUGLU(chain A and (resid -2 through 9 or (resid 10...AA-2 - 96 - 17
12TYRTYRLYSLYS(chain A and (resid -2 through 9 or (resid 10...AA10 - 1118 - 19
13HISHISASNASN(chain A and (resid -2 through 9 or (resid 10...AA-2 - 4776 - 485
14HISHISASNASN(chain A and (resid -2 through 9 or (resid 10...AA-2 - 4776 - 485
15HISHISASNASN(chain A and (resid -2 through 9 or (resid 10...AA-2 - 4776 - 485
16HISHISASNASN(chain A and (resid -2 through 9 or (resid 10...AA-2 - 4776 - 485
21HISHISGLUGLU(chain B and (resid -2 through 9 or (resid 10...BB-2 - 96 - 17
22TYRTYRLYSLYS(chain B and (resid -2 through 9 or (resid 10...BB10 - 1118 - 19
23HISHISASNASN(chain B and (resid -2 through 9 or (resid 10...BB-2 - 4776 - 485
24HISHISASNASN(chain B and (resid -2 through 9 or (resid 10...BB-2 - 4776 - 485
25HISHISASNASN(chain B and (resid -2 through 9 or (resid 10...BB-2 - 4776 - 485
26HISHISASNASN(chain B and (resid -2 through 9 or (resid 10...BB-2 - 4776 - 485
31HISHISARGARG(chain C and (resid -2 through 19 or resid 21...CC-2 - 196 - 27
32SERSERLYSLYS(chain C and (resid -2 through 19 or resid 21...CC21 - 12929 - 137
33GLNGLNLYSLYS(chain C and (resid -2 through 19 or resid 21...CC130 - 131138 - 139
34HISHISASNASN(chain C and (resid -2 through 19 or resid 21...CC-2 - 4776 - 485
35HISHISASNASN(chain C and (resid -2 through 19 or resid 21...CC-2 - 4776 - 485
36HISHISASNASN(chain C and (resid -2 through 19 or resid 21...CC-2 - 4776 - 485
37HISHISASNASN(chain C and (resid -2 through 19 or resid 21...CC-2 - 4776 - 485

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Components

#1: Protein Serine-tRNA ligase


Mass: 55302.875 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: Nfow_scaffold00184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen, B8:25.5% PEG 4000, 15% glycerol, 170mM NaOAc: NafoA.01238.a.B1.PW37973 at 32.5mg/ml + 3mM L-Serine + 3mM AMPPNP + 3mM MgCl2: cryo: direct: tray 286789b8, puck PEM7-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→42.047 Å / Num. obs: 105635 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.457 % / Biso Wilson estimate: 31.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.077 / Χ2: 1.032 / Net I/σ(I): 18.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.157.5610.5444.3177380.8970.584100
2.15-2.217.5610.4515.2375850.9280.484100
2.21-2.287.5790.3836.0973550.9470.411100
2.28-2.357.5820.327.0971690.9620.34499.9
2.35-2.427.550.2528.8169140.9760.271100
2.42-2.517.540.20210.7267210.9830.21799.9
2.51-2.67.5360.16512.6764920.9890.17899.9
2.6-2.717.5280.13615.0262470.9910.14699.9
2.71-2.837.4820.10917.6759760.9940.11799.9
2.83-2.977.5030.09120.6957480.9950.09799.8
2.97-3.137.4510.07424.1954450.9970.07999.8
3.13-3.327.3910.06527.3851520.9970.0799.7
3.32-3.557.3350.05431.548690.9970.05899.7
3.55-3.837.2910.04934.3845350.9980.05399.7
3.83-4.27.2530.04436.8941810.9980.04799.7
4.2-4.77.2250.03839.2437950.9990.04199.5
4.7-5.427.2480.03639.5533540.9990.03999.7
5.42-6.647.3520.03538.6728740.9990.03899.7
6.64-9.397.2330.03140.4422390.9990.03399.6
9.39-42.0476.6770.02840.9312460.9980.0395.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MoRDa3.22phasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3lsq via Morda

3lsq


Resolution: 2.1→42.047 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.01
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1960 1.86 %0
Rwork0.1582 ---
obs0.1588 105584 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.48 Å2 / Biso mean: 40.2529 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 2.1→42.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10450 0 81 1029 11560
Biso mean--32.87 44.42 -
Num. residues----1339
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5767X-RAY DIFFRACTION6.386TORSIONAL
12B5767X-RAY DIFFRACTION6.386TORSIONAL
13C5767X-RAY DIFFRACTION6.386TORSIONAL
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 (%)
2.1-2.15250.21741470.179873207467100
2.1525-2.21070.20371610.174173217482100
2.2107-2.27580.20681210.168573957516100
2.2758-2.34920.24471470.170673747521100
2.3492-2.43320.20881340.165373577491100
2.4332-2.53060.19991300.164573607490100
2.5306-2.64570.21221280.164173897517100
2.6457-2.78520.20771320.16574037535100
2.7852-2.95970.20321140.170674067520100
2.9597-3.18810.20131460.169373947540100
3.1881-3.50880.18941440.158874097553100
3.5088-4.01620.17141650.143673947559100
4.0162-5.05860.16311290.126875087637100
5.0586-42.05590.18981620.17437594775699
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)
10.8478-0.63421.73770.501-1.13915.0795-0.0991-0.23050.04360.13180.1135-0.09930.0163-0.2273-0.02570.3889-0.03280.01130.5035-0.00960.2902-3.731346.839333.9876
21.10250.15430.12590.7834-0.08011.09420.0997-0.03240.12620.0221-0.06150.043-0.1068-0.1805-0.04010.24050.042-0.00160.18620.00730.24981.97563.7913-13.0636
32.8001-0.3595-0.41042.1511-0.0061.96940.0440.49830.1341-0.41280.0805-0.39660.0060.0454-0.17370.41620.01120.09980.31870.06350.313322.899540.2712-41.1015
44.538-0.2131-2.86630.20160.10422.10870.4525-0.76760.4655-0.0024-0.0048-0.7672-0.26460.9281-0.39480.4326-0.09580.14620.86960.02850.846240.387544.6323-37.5455
51.45680.024-0.41830.6421-0.01811.41360.05290.04980.1194-0.0464-0.02110.11640.0001-0.4942-0.03260.1778-0.0079-0.02080.23260.00580.2191-6.299730.8342-7.7871
60.7668-0.2842-0.11180.49930.29391.73170.02820.05650.0572-0.0476-0.0576-0.06070.1083-0.02350.03170.2263-0.0227-0.02170.15790.0230.190215.276524.714-11.0972
71.7414-0.3562-0.59890.9180.22171.87660.05360.19830.0102-0.1364-0.03360.01290.1286-0.1951-0.00190.2246-0.0477-0.03540.1543-0.00580.16384.535125.8402-18.4047
84.8224-2.6714-2.27264.30110.75313.0888-0.1062-0.2436-0.31690.11650.00160.34650.5177-0.37410.12930.3006-0.16260.00680.33690.01330.2435-10.043315.75343.5458
90.6967-0.8746-0.44062.9490.91171.5822-0.02860.0930.0819-0.11130.0279-0.81860.40890.6153-0.10690.4490.14020.10620.5666-0.00750.627151.854760.9386-21.362
101.0590.33170.05231.33960.06030.96580.03570.06290.0275-0.0716-0.0605-0.2243-0.11950.10530.02120.2644-0.0107-0.0090.19860.03370.288128.124274.2902-15.2475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 141 )A-2 - 141
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 477 )A142 - 477
3X-RAY DIFFRACTION3chain 'B' and (resid -2 through 61 )B-2 - 61
4X-RAY DIFFRACTION4chain 'B' and (resid 62 through 141 )B62 - 141
5X-RAY DIFFRACTION5chain 'B' and (resid 142 through 210 )B142 - 210
6X-RAY DIFFRACTION6chain 'B' and (resid 211 through 311 )B211 - 311
7X-RAY DIFFRACTION7chain 'B' and (resid 312 through 451 )B312 - 451
8X-RAY DIFFRACTION8chain 'B' and (resid 452 through 477 )B452 - 477
9X-RAY DIFFRACTION9chain 'C' and (resid -2 through 182 )C-2 - 182
10X-RAY DIFFRACTION10chain 'C' and (resid 183 through 477 )C183 - 477

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