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

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Basic information

Entry
Database: PDB / ID: 6xxm
TitleCrystal Structure of Human Deoxyhypusine Synthase in complex with putrescine
Components(Deoxyhypusine synthase) x 2
KeywordsTRANSFERASE / hypusination / deoxyhypusine synthase / EIF5A / translation / hypusine / posttranslational modification / polyamines / deoxyhypusine
Function / homology
Function and homology information


deoxyhypusine synthase / deoxyhypusine synthase activity / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...deoxyhypusine synthase / deoxyhypusine synthase activity / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / 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
1,4-DIAMINOBUTANE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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)82,4165
Polymers82,1212
Non-polymers2943
Water10,251569
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,83110
Polymers164,2424
Non-polymers5896
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area28280 Å2
ΔGint-157 kcal/mol
Surface area42780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.734, 104.734, 160.672
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Deoxyhypusine synthase / / DHS


Mass: 41044.500 Da / Num. of mol.: 1
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
#2: Protein Deoxyhypusine synthase / / DHS


Mass: 41076.566 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


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


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
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: 60.29 %
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 PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.67→46.12 Å / Num. obs: 118364 / % possible obs: 99.8 % / Redundancy: 10.066 % / Biso Wilson estimate: 33.974 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.112 / Χ2: 1.09 / Net I/σ(I): 14.28 / Num. measured all: 1191506
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
1.67-1.779.7052.5860.9518297518985188530.4962.72999.3
1.77-1.8910.3671.4691.7918461917851178090.7851.54499.8
1.89-2.0410.2490.6983.8117039716632166260.9250.734100
2.04-2.249.660.3566.7914841515378153640.9750.37699.9
2.24-2.510.6180.20312.1114796113938139350.9930.214100
2.5-2.8910.2580.11519.5512654312337123360.9970.121100
2.89-3.539.7190.06133.110183510493104780.9990.06499.9
3.53-4.9810.1960.03953.1783911823782300.9990.04199.9
4.98-46.129.4760.03258.9344850475947330.9990.03499.5

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Processing

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

1dhs


Resolution: 1.67→46.12 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.83
RfactorNum. reflection% reflection
Rfree0.1746 2099 1.77 %
Rwork0.1605 --
obs0.1607 118314 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 243.38 Å2 / Biso mean: 42.214 Å2 / Biso min: 16.07 Å2
Refinement stepCycle: final / Resolution: 1.67→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5408 0 58 570 6036
Biso mean--63.24 47.84 -
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 (%)
1.67-1.710.38241360.35177556769298
1.71-1.750.32041380.306276517789100
1.75-1.80.32091380.281776737811100
1.8-1.850.32131390.256376827821100
1.85-1.910.25871390.234476997838100
1.91-1.980.20911390.196776657804100
1.98-2.060.18991390.174477367875100
2.06-2.150.18691390.16876897828100
2.15-2.270.17321400.150977487888100
2.27-2.410.15191400.142577397879100
2.41-2.590.14131410.134777747915100
2.59-2.850.13831400.134477797919100
2.85-3.270.14661420.139278287970100
3.27-4.120.15111420.133578698011100
4.12-46.120.17051470.157181278274100
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)
10.06760.0063-0.03570.6121-0.0170.0161-0.07120.0575-0.5052-0.14310.12750.283-0.07721.2669-0.07890.845-0.21630.07211.49650.03480.993414.8171-15.446443.6618
21.473-1.3585-0.46821.74650.70660.7336-0.00660.0311-0.0447-0.16360.09730.17150.2677-0.37340.0830.2916-0.1456-0.02150.253-0.00010.242932.4752-25.526920.2545
30.66070.1978-0.45671.108-0.25011.3226-0.11180.14170.0239-0.30780.14030.07250.0022-0.15690.0470.2392-0.0896-0.01230.1585-0.010.147543.4547-1.73891.1402
40.31940.256-0.22161.9085-0.4580.2602-0.07050.09250.1303-0.3280.08670.0547-0.0506-0.18410.04650.3612-0.1026-0.00470.25330.00140.198244.03142.1933-7.376
50.2528-0.13780.17180.80270.02860.5566-0.0565-0.00410.0519-0.1370.08250.1955-0.0688-0.21010.05820.25-0.0621-0.04570.27690.01870.238133.51341.48075.8811
60.7797-0.0656-0.13460.66480.31660.6512-0.03060.08520.079-0.02410.1557-0.1036-0.24720.11280.02740.256-0.00910.00830.1634-0.02090.215851.857723.585428.1744
70.64770.0019-0.03080.75070.12551.0642-0.04330.0330.0235-0.16810.0850.0398-0.2136-0.0892-0.00010.24380.0117-0.02060.16660.01920.189838.653120.664213.5898
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 197 )A54 - 197
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 239 )A198 - 239
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 363 )A240 - 363
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 110 )B28 - 110
7X-RAY DIFFRACTION7chain 'B' and (resid 111 through 363 )B111 - 363

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