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

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Basic information

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


deoxyhypusine synthase / peptidyl-lysine modification to peptidyl-hypusine / Hypusine synthesis from eIF5A-lysine / 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 / peptidyl-lysine modification to peptidyl-hypusine / Hypusine synthesis from eIF5A-lysine / 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 / cytosol / cytoplasm
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 / SPERMIDINE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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: 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 / 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)84,71743
Polymers82,0892
Non-polymers2,62841
Water7,296405
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,43486
Polymers164,1784
Non-polymers5,25682
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area43840 Å2
ΔGint-65 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.980, 104.980, 160.898
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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 , 7 types, 446 molecules

#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


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


Mass: 18.015 Da / Num. of mol.: 405 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix, 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 8, 2019
RadiationMonochromator: 0 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.649→46.194 Å / Num. obs: 123691 / % possible obs: 99.9 % / Redundancy: 11.092 % / Biso Wilson estimate: 34.126 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.116 / Χ2: 1.307 / Net I/σ(I): 12.8
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
1.65-1.7511.1642.3520.9422030419894197340.6722.46599.2
1.75-1.8711.1991.2991.7620831618603186020.861.361100
1.87-2.0210.9110.6573.418982517401173980.950.689100
2.02-2.2111.5690.356.5218539816026160260.9850.366100
2.21-2.4710.9250.19111.3115888714544145440.9940.2100
2.47-2.8511.5420.1218.714879312891128910.9970.125100
2.85-3.4910.9180.07530.2711989610981109810.9980.079100
3.49-4.9210.4750.05244.8889615855685550.9990.055100
4.92-46.19410.2640.04449.7450899496849590.9990.04699.8

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Processing

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

1dhs


Resolution: 1.65→46.194 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.4
RfactorNum. reflection% reflection
Rfree0.1622 2099 1.7 %
Rwork0.1553 --
obs0.1554 123541 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.49 Å2 / Biso mean: 40.2291 Å2 / Biso min: 17.88 Å2
Refinement stepCycle: final / Resolution: 1.65→46.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5362 0 383 405 6150
Biso mean--62.37 44.94 -
Num. residues----691
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.649-1.68710.40331370.3785789498
1.6871-1.72930.32721390.32027990100
1.7293-1.77610.32041380.29078023100
1.7761-1.82830.29461380.25718037100
1.8283-1.88730.25661390.23428008100
1.8873-1.95480.22661390.20028061100
1.9548-2.03310.1851390.17198042100
2.0331-2.12560.15041400.15558064100
2.1256-2.23760.16211390.1438089100
2.2376-2.37780.1451390.13588076100
2.3778-2.56140.1311410.13068125100
2.5614-2.81910.13521400.1318119100
2.8191-3.2270.15851410.13358166100
3.227-4.06530.11691430.13048243100
4.0653-46.1940.15961470.14918505100
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)
10.83380.3574-1.41430.7816-1.85897.38240.02740.10130.3319-0.0858-0.0469-0.0943-0.13010.32590.0330.636-0.0976-0.02160.9436-0.05280.7863-14.744515.689642.1045
23.6147-1.95741.33973.1744-0.81231.3064-0.00070.18870.0161-0.07120.0034-0.1485-0.25980.3312-0.00330.3062-0.1190.02440.31310.01980.2604-33.108725.320820.02
30.82760.0288-0.19871.00920.2261.449-0.13860.2061-0.0178-0.42490.1361-0.2354-0.03440.459-0.01980.3653-0.120.08130.4347-0.01620.3197-25.30188.48341.9105
40.44530.08380.00310.5951-0.02240.8902-0.06360.0891-0.0256-0.22440.075-0.00920.04880.0744-0.00890.3201-0.06410.00650.27060.00180.2245-44.5526-2.8942-0.4086
50.6846-0.59440.38531.37850.03990.7335-0.0855-0.04030.02040.00650.1031-0.160.02650.2124-0.00970.2671-0.01560.02070.3692-0.01590.2996-28.1867-1.416117.1586
63.36550.1995-1.44612.8884-0.02014.5460.06270.09890.3461-0.35870.0561-0.2344-0.40750.1746-0.10830.3235-0.09240.02840.26580.01340.2705-35.835916.04924.3981
71.431-1.05360.89071.8283-0.84411.65870.0004-0.0778-0.15380.15750.07190.08110.2532-0.0127-0.04210.32460.05410.01780.23670.02410.2452-48.5286-17.995246.0971
82.00280.56740.52541.1623-0.17290.7953-0.01350.278-0.2608-0.16680.14660.10390.3325-0.1679-0.13390.3472-0.0351-0.03130.25320.00630.2575-53.7578-25.830420.9618
90.5288-0.00160.03860.6461-0.10010.9407-0.04060.0425-0.0601-0.1520.0673-0.07880.24020.135-0.0260.3140.0160.01720.2536-0.0150.2388-39.0836-20.790313.637
104.16932.52181.81726.0312-0.73124.1789-1.48911.41-0.1002-2.50282.21131.02360.4039-2.4328-0.72791.34680.0917-0.08951.35040.0271.1337-46.8493-42.555720.9984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 27 )A9 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 53 )A28 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 88 )A54 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 307 )A89 - 307
5X-RAY DIFFRACTION5chain 'A' and (resid 308 through 342 )A308 - 342
6X-RAY DIFFRACTION6chain 'A' and (resid 343 through 363 )A343 - 363
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 53 )B28 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 110 )B54 - 110
9X-RAY DIFFRACTION9chain 'B' and (resid 111 through 363 )B111 - 363
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 364 )B364

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