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- PDB-7n4d: Translation initiation factor eif-5a family protein from Naegleri... -

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Basic information

Entry
Database: PDB / ID: 7n4d
TitleTranslation initiation factor eif-5a family protein from Naegleria fowleri ATCC 30863
ComponentsEukaryotic translation initiation factor 5A
KeywordsGENE REGULATION / SSGCID / eif5a / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / ribosome binding
Similarity search - Function
Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5A
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Translation initiation factor eif-5a family protein from Naegleria fowleri ATCC 30863
Authors: Sroge, C.D. / Davies, D.R. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E. / Abendroth, J.
History
DepositionJun 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Eukaryotic translation initiation factor 5A
B: Eukaryotic translation initiation factor 5A
C: Eukaryotic translation initiation factor 5A
D: Eukaryotic translation initiation factor 5A


Theoretical massNumber of molelcules
Total (without water)68,9224
Polymers68,9224
Non-polymers00
Water99155
1
A: Eukaryotic translation initiation factor 5A


Theoretical massNumber of molelcules
Total (without water)17,2301
Polymers17,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5A


Theoretical massNumber of molelcules
Total (without water)17,2301
Polymers17,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Eukaryotic translation initiation factor 5A


Theoretical massNumber of molelcules
Total (without water)17,2301
Polymers17,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Eukaryotic translation initiation factor 5A


Theoretical massNumber of molelcules
Total (without water)17,2301
Polymers17,2301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.570, 58.940, 102.340
Angle α, β, γ (deg.)90.000, 93.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 through 27 or (resid 28...
21(chain B and (resid 16 through 26 or (resid 27...
31(chain C and (resid 16 through 27 or (resid 28...
41(chain D and (resid 16 through 26 or (resid 27...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 16 through 27 or (resid 28...A16 - 27
121(chain A and (resid 16 through 27 or (resid 28...A28
131(chain A and (resid 16 through 27 or (resid 28...A16 - 157
141(chain A and (resid 16 through 27 or (resid 28...A16 - 157
151(chain A and (resid 16 through 27 or (resid 28...A16 - 157
161(chain A and (resid 16 through 27 or (resid 28...A16 - 157
211(chain B and (resid 16 through 26 or (resid 27...B16 - 26
221(chain B and (resid 16 through 26 or (resid 27...B27 - 28
231(chain B and (resid 16 through 26 or (resid 27...B16 - 157
241(chain B and (resid 16 through 26 or (resid 27...B16 - 157
251(chain B and (resid 16 through 26 or (resid 27...B16 - 157
261(chain B and (resid 16 through 26 or (resid 27...B0
271(chain B and (resid 16 through 26 or (resid 27...B16 - 157
281(chain B and (resid 16 through 26 or (resid 27...B16 - 157
291(chain B and (resid 16 through 26 or (resid 27...B16 - 157
2101(chain B and (resid 16 through 26 or (resid 27...B16 - 157
311(chain C and (resid 16 through 27 or (resid 28...C16 - 27
321(chain C and (resid 16 through 27 or (resid 28...C28
331(chain C and (resid 16 through 27 or (resid 28...C16 - 157
341(chain C and (resid 16 through 27 or (resid 28...C16 - 157
351(chain C and (resid 16 through 27 or (resid 28...C16 - 157
361(chain C and (resid 16 through 27 or (resid 28...C16 - 157
411(chain D and (resid 16 through 26 or (resid 27...D16 - 26
421(chain D and (resid 16 through 26 or (resid 27...D27 - 28
431(chain D and (resid 16 through 26 or (resid 27...D16 - 157
441(chain D and (resid 16 through 26 or (resid 27...D16 - 157
451(chain D and (resid 16 through 26 or (resid 27...D16 - 157
461(chain D and (resid 16 through 26 or (resid 27...D16 - 157

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Components

#1: Protein
Eukaryotic translation initiation factor 5A / eIF-5A


Mass: 17230.420 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: FDP41_013076 / Plasmid: NafoA.20237.a.D11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6A5BRA8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: Rigaku JCSG+ screen, D12:0.04M KPO4, 16% w/v PEG 8 000, 20% glycerol: NafoA.20237.a.D11.PD38375 NafoA.01541.a.B2.PW38668 (4:1) at 13.91 mg/ml + 4mM GC7,deoxyhypusine synthase inhibitor + 4mM ...Details: Rigaku JCSG+ screen, D12:0.04M KPO4, 16% w/v PEG 8 000, 20% glycerol: NafoA.20237.a.D11.PD38375 NafoA.01541.a.B2.PW38668 (4:1) at 13.91 mg/ml + 4mM GC7,deoxyhypusine synthase inhibitor + 4mM NAD: cryo: direct: tray 320284d12, puck pvq5-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 25, 2021 / 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: 2.45→31.36 Å / Num. obs: 24974 / % possible obs: 98.2 % / Redundancy: 2.64 % / Biso Wilson estimate: 42.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.084 / Χ2: 0.925 / Net I/σ(I): 11.39 / Num. measured all: 65938 / Scaling rejects: 6
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
2.45-2.512.6450.5272.114914186818580.7920.65799.5
2.51-2.582.6550.5152.174792181518050.7530.64399.4
2.58-2.662.6290.4422.644590176117460.8090.55499.1
2.66-2.742.6630.3453.264615174617330.8740.4399.3
2.74-2.832.6430.2564.154321164716350.9190.3299.3
2.83-2.932.6390.1985.214241162016070.9520.24899.2
2.93-3.042.6630.1596.574135156515530.9650.19999.2
3.04-3.162.6550.1268.183908148514720.980.15799.1
3.16-3.32.6420.09810.143775145614290.9870.12398.1
3.3-3.462.6390.07212.923573137213540.9920.0998.7
3.46-3.652.6450.06115.563402131212860.9930.07698
3.65-3.872.6330.04818.193215124312210.9960.05998.2
3.87-4.142.6360.04220.223026117611480.9970.05297.6
4.14-4.472.6350.03523.552798109710620.9980.04496.8
4.47-4.92.5930.03125.39252010089720.9980.03996.4
4.9-5.482.6410.03225.0623279148810.9980.03996.4
5.48-6.332.6680.03523.4720768167780.9970.04495.3
6.33-7.752.650.02925.5417256806510.9980.03695.7
7.75-10.962.5840.02531.2913365465170.9980.03294.7
10.96-31.362.440.02333.146493162660.9980.02984.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5dlq as per Morda

5dlq


Resolution: 2.45→31.36 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 2021 8.1 %
Rwork0.2339 22942 -
obs0.2387 24963 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.67 Å2 / Biso mean: 58.9055 Å2 / Biso min: 32.17 Å2
Refinement stepCycle: final / Resolution: 2.45→31.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 0 55 4184
Biso mean---52.83 -
Num. residues----551
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2409X-RAY DIFFRACTION10.286TORSIONAL
12B2409X-RAY DIFFRACTION10.286TORSIONAL
13C2409X-RAY DIFFRACTION10.286TORSIONAL
14D2409X-RAY DIFFRACTION10.286TORSIONAL
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 (%)
2.45-2.510.38041480.32441641178999
2.51-2.580.36071330.32371657179099
2.58-2.650.40231540.31071620177499
2.66-2.740.29681480.29761663181199
2.74-2.840.35681540.28841603175799
2.84-2.950.34541650.29611639180499
2.95-3.090.33751760.25581610178699
3.09-3.250.33051150.25581673178899
3.25-3.450.31791060.25091694180098
3.45-3.720.28481670.21881602176998
3.72-4.090.23541540.21191626178097
4.09-4.680.25151520.19111606175897
4.68-5.890.2771350.19631642177796
5.89-31.360.26961140.20651666178094
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)
18.24490.27853.92783.8541-0.74095.7208-0.0148-0.1892-0.275-0.15090.16940.1877-0.14690.1694-0.07630.42520.1257-0.01950.53380.12650.3881-9.58032.257734.6575
23.41360.78444.11442.1290.98175.06920.0662-0.8444-0.28820.06890.3220.5832-0.2365-0.4066-0.22810.35660.03330.04860.86160.16390.6691-20.84820.795936.7389
32.644-1.5851.51412.1366-0.15841.1517-0.0566-1.0589-0.10110.34370.27860.5037-0.0651-0.05240.01310.32440.06650.00640.88970.20740.5031-12.04573.623639.7633
44.5827-0.59261.01712.2135-0.25632.1882-0.179-0.1136-0.01090.3818-0.1209-0.08630.0030.16910.00520.3047-0.0667-0.07720.6198-0.05680.313215.7888-1.441546.6399
54.0048-0.95860.26971.83140.52361.2325-0.006-0.46820.43950.43560.0692-0.2985-0.3213-0.18780.03410.4040.0124-0.06080.4752-0.00620.373812.5075-0.355351.4907
65.2485-1.47562.09184.35210.97022.7184-0.2114-0.66280.17050.20940.54270.23610.5403-0.5645-0.05420.19460.00370.02660.5760.09570.367211.1204-4.28146.9568
76.1584-2.55190.61286.2465-1.83062.75510.1932-0.47940.0521-0.0974-0.2730.03290.4143-0.37790.02340.3699-0.0252-0.0170.66610.09360.17387.9553-3.973847.9642
89.20251.2207-5.42862.17390.03636.35470.08161.26290.777-0.21940.0151-0.1578-0.14840.0315-0.15620.37260.01960.06380.72650.21520.5608-39.409215.300212.5208
93.61340.72260.89232.94820.26315.2818-0.14190.4573-0.3598-0.25320.3277-0.1204-0.2870.0593-0.10760.3672-0.00330.09220.7483-0.04440.3918-13.067220.09231.5267
106.6434-6.07415.48675.4823-4.60945.74880.6527-0.0858-0.6259-0.62010.05020.63260.4177-0.5533-0.6390.59660.0623-0.03560.61090.13930.478718.9981-27.082137.449
111.9847-0.19790.55655.4446-1.10454.42520.19380.45650.1435-0.7918-0.4315-0.25270.287-0.07650.30010.33580.06080.06570.59140.04840.307212.4636-3.836125.3207
124.95440.0689-1.55027.1581-0.57273.7682-1.23471.17280.3296-1.17760.61280.1035-0.0234-0.01220.17730.8374-0.3528-0.06191.12620.35680.7559-5.8908-17.53335.6878
138.29871.8655-2.00814.7622-1.13164.6730.01080.36011.3773-0.52480.56010.6281-0.3656-0.10420.13640.4598-0.11220.0491.01730.32550.8149-7.019-15.552514.0322
143.24692.5202-1.01293.6482-1.10383.9951-0.00050.49010.9871.37690.21841.43980.02010.02850.06980.5398-0.19830.11260.69160.12460.6882-7.2281-14.029318.9796
154.03442.5533-1.80124.4232-0.17911.1157-0.0228-0.01850.5613-0.79930.4279-0.1372-0.8713-0.153-0.08420.7056-0.1634-0.10731.06260.34440.5796-3.4279-12.416111.9936
163.88780.64340.27847.201-1.94322.6545-0.0073-0.3678-0.19830.2460.119-0.0248-0.045-0.30520.01010.30360.017-0.07250.71130.04440.2887-12.1841-41.154822.9186
173.1180.6163-0.40826.49410.95851.58230.2162-0.0305-0.06240.16980.1426-0.6526-0.36110.1126-0.0140.3538-0.00470.04250.59490.01860.3526-8.5334-39.820421.9886
182.79881.94530.60472.90010.13310.91970.1908-0.7272-0.44461.7474-0.1165-0.4286-0.1337-0.1353-0.02470.6337-0.06260.00530.69860.00940.3295-14.8811-36.430234.1288
194.46871.2374-0.21394.1766-1.52852.59640.03490.3560.64850.08680.40980.5389-0.57560.0188-0.00510.3705-0.0501-0.01170.54810.04580.27-14.2623-35.568521.5984
207.011.6102-1.81566.9176-0.96933.76370.4345-0.72420.2088-0.0629-0.34940.3638-0.32550.42930.04940.35850.0432-0.02460.70720.12510.3572-14.638-33.146223.8501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 36 )A16 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 55 )A37 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 85 )A56 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 103 )A86 - 103
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 134 )A104 - 134
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 148 )A135 - 148
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 157 )A149 - 157
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 85 )B16 - 85
9X-RAY DIFFRACTION9chain 'B' and (resid 86 through 157 )B86 - 157
10X-RAY DIFFRACTION10chain 'C' and (resid 16 through 85 )C16 - 85
11X-RAY DIFFRACTION11chain 'C' and (resid 86 through 157 )C86 - 157
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 25 )D16 - 25
13X-RAY DIFFRACTION13chain 'D' and (resid 26 through 36 )D26 - 36
14X-RAY DIFFRACTION14chain 'D' and (resid 37 through 68 )D37 - 68
15X-RAY DIFFRACTION15chain 'D' and (resid 69 through 85 )D69 - 85
16X-RAY DIFFRACTION16chain 'D' and (resid 86 through 103 )D86 - 103
17X-RAY DIFFRACTION17chain 'D' and (resid 104 through 119 )D104 - 119
18X-RAY DIFFRACTION18chain 'D' and (resid 120 through 135 )D120 - 135
19X-RAY DIFFRACTION19chain 'D' and (resid 136 through 148 )D136 - 148
20X-RAY DIFFRACTION20chain 'D' and (resid 149 through 157 )D149 - 157

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