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- PDB-6xxl: Crystal Structure of Human Deoxyhypusine Synthase in complex with... -

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Basic information

Entry
Database: PDB / ID: 6xxl
TitleCrystal Structure of Human Deoxyhypusine Synthase in complex with spermine
ComponentsDeoxyhypusine synthase
KeywordsTRANSFERASE / hypusination / deoxyhypusine synthase / EIF5A / translation / hypusine / posttranslational modification / polyamines / deoxyhypusine / spermine
Function / homology
Function and homology information


deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / FORMIC ACID / OXAMIC ACID / SPERMINE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWator, E. / Wilk, P. / Grudnik, P.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/33/B/NZ1/01839 Poland
CitationJournal: Biomolecules / Year: 2020
Title: Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase.
Authors: Wator, E. / Wilk, P. / Grudnik, P.
History
DepositionJan 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,69422
Polymers82,0892
Non-polymers1,60520
Water8,521473
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,38844
Polymers164,1784
Non-polymers3,21040
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area33180 Å2
ΔGint-94 kcal/mol
Surface area41530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.898, 104.898, 160.429
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-735-

HOH

21B-709-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Deoxyhypusine synthase / DHS


Mass: 41044.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49366, deoxyhypusine synthase

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Non-polymers , 8 types, 493 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#8: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix (MPD, PEG 3350, PEG 1000), 100 mM Tris-Bicine pH = 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.688→46.085 Å / Num. obs: 114776 / % possible obs: 99.8 % / Redundancy: 19.899 % / Biso Wilson estimate: 40.186 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.108 / Χ2: 1.27 / Net I/σ(I): 17.69
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
1.69-1.7920.1244.3330.7536577918409181760.5894.44498.7
1.79-1.9119.3842.1321.5433550417317173080.8392.18999.9
1.91-2.0720.7450.9713.5633493316147161450.9540.995100
2.07-2.2620.1070.4737.0229905614879148730.9880.486100
2.26-2.5320.0590.24413.1127111313519135160.9960.25100
2.53-2.9220.2680.13323.4924334312013120060.9980.13799.9
2.92-3.5719.7850.06844.520109510167101640.9990.07100
3.57-5.0418.4270.04568.84147008798379780.9990.04699.9
5.04-46.08518.6740.03679.77860864621461010.03799.8

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Processing

Software
NameVersionClassification
PHENIXv.1.17.1refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXv.1.17.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DHS

1dhs


Resolution: 1.69→46.085 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.1793 2099 1.83 %
Rwork0.1617 --
obs0.162 114614 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 228.16 Å2 / Biso mean: 52.1273 Å2 / Biso min: 23.49 Å2
Refinement stepCycle: final / Resolution: 1.69→46.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5289 0 236 473 5998
Biso mean--75.61 57.59 -
Num. residues----672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.69-1.72680.43431340.4115719996
1.7268-1.770.43351390.36227408100
1.77-1.81780.36131380.32347429100
1.8178-1.87130.33751400.29147459100
1.8713-1.93170.29471380.25287449100
1.9317-2.00080.22591390.2087454100
2.0008-2.08090.19111390.1797466100
2.0809-2.17560.18511390.16877463100
2.1756-2.29030.17451400.15497495100
2.2903-2.43370.19771400.14677506100
2.4337-2.62160.16091410.14177524100
2.6216-2.88540.17941410.1427554100
2.8854-3.30290.15891410.14577581100
3.3029-4.16080.15791420.13087636100
4.1608-46.0850.14931480.15427892100
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)
10.03750.0905-0.00250.14510.01160.24920.17060.00650.2012-0.2238-0.0782-0.0375-0.5097-0.25720.03890.6060.08510.02310.26970.01030.4074-37.3572-14.6738-6.3383
20.75310.14680.29690.1708-0.01610.14720.08880.25220.2231-0.4134-0.2695-0.261-0.37540.261-0.45020.73320.07880.13280.3430.1180.4703-19.8549-17.408-25.2117
30.6703-0.39040.14520.5670.40140.95680.17020.1399-0.0796-0.1907-0.16960.0470.03670.0205-0.00020.44430.1002-0.02460.2811-0.00940.3052-24.6125-43.2658-25.4886
40.02030.0007-0.0230.090.03080.02220.16310.21540.0784-0.4731-0.1760.0553-0.1181-0.006200.55870.15630.02010.41770.01450.2834-15.749-42.4302-38.0224
5-0.0231-0.1461-0.12990.16520.18120.48430.17060.2364-0.074-0.2602-0.162-0.03570.00240.152900.47570.10440.01860.35690.01870.3276-15.5618-41.3807-31.7999
60.1079-0.08860.03490.0468-0.01840.01820.09280.15760.1863-0.1936-0.0923-0.239-0.27910.332700.5067-0.02220.07190.33820.04930.4057-12.5707-25.0892-20.6011
70.0132-0.00350.00430.0371-0.05470.0423-0.03650.01320.2246-0.21230.12770.18580.0202-0.104700.5634-0.07250.0090.48480.02140.4813-10.7261-28.2362-7.3184
80.3086-0.0799-0.10480.1333-0.11610.20270.16180.04560.2216-0.0559-0.1355-0.0566-0.24330.07460.00360.48460.03990.03970.25360.04490.3679-25.3739-22.1347-18.5149
91.07690.0780.25060.4652-0.50420.54930.0566-0.122-0.1773-0.00040.03030.08450.49910.16980.01060.30660.0357-0.04090.34490.02930.3255-7.43-57.6166.9138
100.13610.17860.00660.13520.00920.1073-0.05110.110.0142-0.15160.2883-0.25710.05050.374200.40340.03440.00730.4301-0.03260.3654-0.8348-53.0577-11.6727
110.9214-0.19530.04870.5374-0.24871.56470.14420.18070.058-0.2126-0.1188-0.08080.02450.429400.28560.02050.05240.42760.02850.30291.3433-42.2422-16.1763
120.20890.1486-0.04630.39260.41880.72020.1974-0.06680.0026-0.1046-0.13210.1340.05650.018900.34420.0124-0.03680.35850.01150.347-11.2276-51.1755-2.3788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 53 )A26 - 53
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 88 )A54 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 196 )A89 - 196
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 214 )A197 - 214
5X-RAY DIFFRACTION5chain 'A' and (resid 215 through 271 )A215 - 271
6X-RAY DIFFRACTION6chain 'A' and (resid 272 through 307 )A272 - 307
7X-RAY DIFFRACTION7chain 'A' and (resid 308 through 327 )A308 - 327
8X-RAY DIFFRACTION8chain 'A' and (resid 328 through 363 )A328 - 363
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 87 )B28 - 87
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 110 )B88 - 110
11X-RAY DIFFRACTION11chain 'B' and (resid 111 through 307 )B111 - 307
12X-RAY DIFFRACTION12chain 'B' and (resid 308 through 364 )B308 - 364

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