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- PDB-1dhs: CRYSTAL STRUCTURE OF THE NAD COMPLEX OF HUMAN DEOXYHYPUSINE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1dhs
TitleCRYSTAL STRUCTURE OF THE NAD COMPLEX OF HUMAN DEOXYHYPUSINE SYNTHASE
ComponentsDEOXYHYPUSINE SYNTHASE
KeywordsTRANSFERASE / SPERMIDINE / INITIATION FACTOR 5A / NAD / SUBUNIT INTERACTIONS / OXIDOREDUCTASE
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 / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.2 Å
AuthorsLiao, D.-I. / Davies, D.R.
CitationJournal: Structure / Year: 1998
Title: Crystal structure of the NAD complex of human deoxyhypusine synthase: an enzyme with a ball-and-chain mechanism for blocking the active site.
Authors: Liao, D.I. / Wolff, E.C. / Park, M.H. / Davies, D.R.
History
DepositionOct 28, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 23, 2021Group: Derived calculations / Structure summary / Category: entity / struct_keywords / struct_site
Item: _entity.pdbx_ec / _struct_keywords.pdbx_keywords ..._entity.pdbx_ec / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7432
Polymers40,0791
Non-polymers6631
Water4,810267
1
A: DEOXYHYPUSINE SYNTHASE
hetero molecules

A: DEOXYHYPUSINE SYNTHASE
hetero molecules

A: DEOXYHYPUSINE SYNTHASE
hetero molecules

A: DEOXYHYPUSINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,9718
Polymers160,3184
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area33400 Å2
ΔGint-199 kcal/mol
Surface area40480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.300, 108.300, 69.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein DEOXYHYPUSINE SYNTHASE /


Mass: 40079.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P49366, deoxyhypusine synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.47 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.5 / Details: 9.0 MG/ML PROTEIN IN 1.7M PHOSPHATE FINAL PH 4.5
Crystal grow
*PLUS
Temperature: 20 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.50 mg/mlprotein1drop
20.05 MNAD1drop
30.05 M1,7-diaminoheptane1drop
40.85 Msodium potassium phosphate1drop
550 mMHEPES1drop
61.7 Msodium potassium phosphate1reservoir
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 15, 1996 / Details: MSC MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18479 / % possible obs: 86.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3.1 / % possible all: 41.9
Reflection
*PLUS
Num. measured all: 108771

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→6 Å / Rfactor Rfree error: 0.6 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1614 10 %RANDOM
Rwork0.153 ---
obs0.153 16140 83.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 44 267 2988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.492
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.352
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2825 89 10.6 %
Rwork0.2173 834 -
obs--43.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.802
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.352

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