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- PDB-6p4v: 1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofa... -

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Basic information

Entry
Database: PDB / ID: 6p4v
Title1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7
ComponentsDeoxyhypusine synthase
KeywordsTRANSFERASE/INHIBITOR / Deoxyhypusine / NAD cofactor / hypusine / spermidine / GC7 / transferase / TRANSFERASE-INHIBITOR complex
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 / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-GUANIDINIUM-7-AMINOHEPTANE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKlein, M.G. / Ambrus-Aikelin, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Novel Allosteric Inhibitors of Deoxyhypusine Synthase.
Authors: Tanaka, Y. / Kurasawa, O. / Yokota, A. / Klein, M.G. / Ono, K. / Saito, B. / Matsumoto, S. / Okaniwa, M. / Ambrus-Aikelin, G. / Morishita, D. / Kitazawa, S. / Uchiyama, N. / Ogawa, K. / Kimura, H. / Imamura, S.
History
DepositionMay 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,2217
Polymers82,4272
Non-polymers1,7945
Water5,873326
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,44214
Polymers164,8544
Non-polymers3,58710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area30810 Å2
ΔGint-127 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.466, 104.466, 159.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-744-

HOH

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Components

#1: Protein Deoxyhypusine synthase / DHS


Mass: 41213.613 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 (E. coli) / References: UniProt: P49366, deoxyhypusine synthase
#2: 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
#3: Chemical ChemComp-GC7 / 1-GUANIDINIUM-7-AMINOHEPTANE


Mass: 174.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H22N4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M TRIS (8.0) AND 65% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 120192 / % possible obs: 99.9 % / Redundancy: 5.6 % / Net I/σ(I): 12
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 241

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0025refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RLZ.PDB

1rlz


Resolution: 1.65→43.73 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.113 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.175 6006 5 %RANDOM
Rwork0.161 ---
obs0.162 113578 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å20 Å2
2--1.44 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5119 0 120 326 5565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195409
X-RAY DIFFRACTIONr_bond_other_d0.0010.025081
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9777357
X-RAY DIFFRACTIONr_angle_other_deg0.757311648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99424.28243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08915885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7041534
X-RAY DIFFRACTIONr_chiral_restr0.0720.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021272
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 444 -
Rwork0.238 7957 -
obs--94.95 %
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)
10.31020.0694-0.04210.756-0.06450.9325-0.0634-0.03240.08560.1020.0874-0.022-0.25090.0759-0.0240.09980.0004-0.01840.0266-0.00760.0749-41.946721.05535.9709
20.23460.038-0.03460.7340.10860.9437-0.0801-0.0752-0.01380.21880.0947-0.0640.04290.1252-0.01450.10520.0649-0.01570.06050.00560.0549-39.6677-1.999248.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 363
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION1A601 - 771
4X-RAY DIFFRACTION2B601 - 755
5X-RAY DIFFRACTION2B28 - 363
6X-RAY DIFFRACTION2B501 - 502

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