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- PDB-6xxi: Crystal Structure of Human Deoxyhypusine Synthase in complex with NAD -

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Basic information

Entry
Database: PDB / ID: 6xxi
TitleCrystal Structure of Human Deoxyhypusine Synthase in complex with NAD
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.679 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)85,83642
Polymers82,0892
Non-polymers3,74740
Water6,413356
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,67384
Polymers164,1784
Non-polymers7,49580
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area42290 Å2
ΔGint-85 kcal/mol
Surface area40090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.819, 104.819, 160.499
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-1368-

HOH

21B-1757-

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 , 7 types, 396 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#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.: 1 / 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.: 356 / 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: 60.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: 1.679→46.091 Å / Num. obs: 116359 / % possible obs: 99.7 % / Redundancy: 8.419 % / Biso Wilson estimate: 34.007 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.135 / Χ2: 1.042 / Net I/σ(I): 8.88
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
1.68-1.788.5562.0210.9215903918694185880.7372.15399.4
1.78-1.98.2211.1741.614425417556175460.8761.25499.9
1.9-2.068.5840.6053.214043916380163600.950.64599.9
2.06-2.258.4440.3425.5112739215089150870.9780.365100
2.25-2.528.3550.2028.9111413113692136610.9840.21699.8
2.52-2.98.5420.1313.7210386712163121590.990.139100
2.9-3.558.4480.08720.798681610321102770.9930.09399.6
3.55-5.018.2330.07127.0166272810380500.9940.07699.3
5.01-46.0918.0850.07228.6437441468246310.9940.07798.9

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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: 1.679→46.091 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.92
RfactorNum. reflection% reflection
Rfree0.1662 2097 1.8 %
Rwork0.1539 --
obs0.1541 116219 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 227.74 Å2 / Biso mean: 43.2395 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 1.679→46.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 494 356 6062
Biso mean--65.3 45.84 -
Num. residues----666
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.679-1.71810.39261360.3554746298
1.7181-1.7610.31441380.31557504100
1.761-1.80860.28741400.28597596100
1.8086-1.86190.30791380.25047512100
1.8619-1.9220.27251370.23267503100
1.922-1.99070.24491390.19047557100
1.9907-2.07040.18791400.16387602100
2.0704-2.16460.1691400.15687607100
2.1646-2.27870.14991390.14187589100
2.2787-2.42150.15031400.13567573100
2.4215-2.60840.14171400.13017632100
2.6084-2.87090.15561400.13317646100
2.8709-3.28620.14431410.135767499
3.2862-4.13980.14191430.12437738100
4.1398-46.0910.14161460.1485792799
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)
14.5642-4.66182.45476.9976-1.79733.3510.04060.15360.1537-0.14370.0545-0.2467-0.33320.31480.00250.3079-0.16170.04360.30510.01920.2623-32.675325.420620.1554
21.5004-0.9808-3.08360.75111.84956.590.0014-0.0904-0.0269-0.24040.0191-0.2508-0.57090.7443-0.13420.257-0.13320.04260.3686-0.00830.2975-27.458212.756111.0631
35.81840.0685-1.2484.7572-2.5451.82-0.15830.9339-0.4703-1.44430.2496-0.54320.01590.4814-0.10580.708-0.12350.19160.694-0.09130.3912-25.03362.2031-10.0446
40.63410.1172-0.09341.0330.15741.7807-0.0740.09740.0004-0.27730.08390.06790.0508-0.06620.02270.3046-0.0827-0.0270.2450.02120.1972-49.4031-1.1576-0.6142
50.58420.12970.36081.03580.34671.6163-0.0310.0532-0.0342-0.17170.0792-0.18430.11280.2767-0.05630.2513-0.0310.05220.2754-0.01090.2178-34.1413-6.64755.1832
64.7023-1.45750.17434.4989-0.57722.23330.08080.14810.251-0.4093-0.0093-0.3919-0.14730.28980.0090.2535-0.12580.03710.2953-0.03390.2262-31.673310.56398.3761
71.8580.88731.14442.89131.3143.213-0.05290.0314-0.121-0.02670.14680.22870.3473-0.2067-0.0640.2435-0.00220.02340.21650.05270.2211-53.807-22.510833.2959
84.0027-1.6525-1.07561.8938-0.93571.861-0.06750.3846-0.3123-0.32120.0710.11280.5068-0.1186-0.10860.4112-0.0159-0.00190.2733-0.02320.1722-46.4812-25.985315.252
90.5798-0.0531-0.00620.8557-0.09151.3826-0.03520.0484-0.0787-0.20360.0766-0.09860.30590.1687-0.03720.3120.0230.02370.2466-0.01350.226-39.0701-20.88213.6146
103.8775-0.9753-0.5364.8762-3.65684.760210.7366-11.4762-25.29378.7873-7.7133-16.67149.34621.6233-3.00961.2445-0.3932-0.19511.12010.12491.5386-47.8221-44.136523.5864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 53 )A28 - 53
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 73 )A54 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 97 )A74 - 97
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 239 )A98 - 239
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 327 )A240 - 327
6X-RAY DIFFRACTION6chain 'A' and (resid 328 through 363 )A328 - 363
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 87 )B28 - 87
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 110 )B88 - 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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