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

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Basic information

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


peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase / 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 ...peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / TRIETHYLENE GLYCOL / SPERMIDINE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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)85,40131
Polymers82,0892
Non-polymers3,31229
Water10,683593
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,80262
Polymers164,1784
Non-polymers6,62458
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area42710 Å2
ΔGint-106 kcal/mol
Surface area41180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.486, 105.486, 160.831
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-783-

HOH

21B-751-

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 , 10 types, 622 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#8: 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
#9: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix (MPD, PEG 1000, PEG 3350), 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.41→46.24 Å / Num. obs: 198798 / % possible obs: 99.8 % / Redundancy: 9.791 % / Biso Wilson estimate: 27.396 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.094 / Χ2: 1.363 / Net I/σ(I): 13.34 / Num. measured all: 1946524
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
1.41-1.499.7292.4370.7630838431896316960.5482.57399.4
1.49-1.610.1781.3051.5230602830069300680.7921.375100
1.6-1.739.6440.672.8626928627989279220.9270.70899.8
1.73-1.8910.3950.3695.5526838825819258190.9780.389100
1.89-2.119.9970.18911.3723411923422234180.9920.199100
2.11-2.449.8780.10721.220422220718206750.9970.11399.8
2.44-2.989.4040.0732.2716541817593175910.9980.074100
2.98-4.218.7670.04646.9312050613766137460.9990.04999.9
4.21-46.248.9240.03456.2570173788178630.9990.03699.8

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Processing

Software
NameVersionClassification
PHENIXv1.17.1refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERv1.17.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DHS

1dhs


Resolution: 1.41→46.24 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1598 2099 1.06 %
Rwork0.1425 196567 -
obs0.1427 198666 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.81 Å2 / Biso mean: 29.4261 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 1.41→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 0 215 593 6184
Biso mean--45.54 38.63 -
Num. residues----692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.41-1.440.36521370.3729127731291098
1.44-1.480.34311390.32321301213151100
1.48-1.520.31091390.28171301713156100
1.52-1.560.23641390.2441300813147100
1.56-1.610.25941390.22541304413183100
1.61-1.670.22261380.1951303613174100
1.67-1.740.1831390.1823129751311499
1.74-1.820.1561400.161310913249100
1.82-1.910.16651390.14411306113200100
1.91-2.030.14691400.12881311013250100
2.03-2.190.13321400.12651307713217100
2.19-2.410.13941410.11851317713318100
2.41-2.760.12381410.11881320913350100
2.76-3.470.15291410.12451327813419100
3.47-46.240.14621470.12551368113828100
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)
11.6191-0.33031.67541.7095-1.6586.7609-0.0697-0.08230.404-0.18610.04550.2964-0.37810.00660.01140.7305-0.0947-0.02730.3758-0.08180.5592-21.5234-5.348615.922
23.73940.98490.96860.95580.86761.1031-0.00860.03740.2078-0.14410.0309-0.0401-0.3576-0.10370.00250.33630.06670.00050.16940.01550.2312-38.5927-15.844-6.2771
31.1602-0.362-0.00930.8206-0.12680.80760.13540.28510.2353-0.3645-0.1638-0.1665-0.33530.0786-0.08380.45560.02290.07040.21630.06150.2944-19.7636-18.1997-25.2601
40.515-0.1216-0.01120.3667-0.00530.83430.08470.09180.0247-0.1529-0.0764-0.0402-0.04580.0823-0.00610.23560.04470.01330.15020.01250.1648-18.9578-38.4255-25.0699
52.73110.2495-0.3163.4899-1.25832.9620.21050.34830.3196-0.2112-0.04880.2765-0.3087-0.2137-0.13740.31610.08310.01050.18310.0320.2314-32.0144-23.3792-22.5419
62.0107-0.04480.57890.27850.14881.39930.0482-0.1195-0.08090.0318-0.0004-0.03280.12370.1889-0.03360.16460.0126-0.00990.28640.02010.2108-8.4137-51.46518.9206
70.7751-0.1989-0.10561.48660.66811.37620.04420.0818-0.1575-0.10450.0479-0.07010.37620.1521-0.07250.25090.0497-0.03160.2145-0.00380.2065-6.7011-63.4863-2.6013
80.96850.65740.32551.6708-0.28910.8356-0.01920.1443-0.1059-0.31480.1135-0.32750.1220.2652-0.12350.2190.03350.0360.2764-0.0220.2158-1.0892-53.0974-11.1899
90.5744-0.11230.10570.5516-0.08030.99080.08450.09950.0701-0.1358-0.0685-0.1201-0.02510.3262-0.01790.1820.02050.04110.28170.01370.20421.1078-42.714-15.9732
101.1652-0.07740.55010.55730.18071.0360.1423-0.0245-0.066-0.0202-0.0656-0.0370.10570.1303-0.07490.1890.0101-0.00360.19260.0110.1839-11.7085-51.5374-2.1897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 27 )A8 - 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 342 )A89 - 342
5X-RAY DIFFRACTION5chain 'A' and (resid 343 through 363 )A343 - 363
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 53 )B28 - 53
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 87 )B54 - 87
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 110 )B88 - 110
9X-RAY DIFFRACTION9chain 'B' and (resid 111 through 307 )B111 - 307
10X-RAY DIFFRACTION10chain 'B' and (resid 308 through 363 )B308 - 363

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