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- PDB-1rlz: Deoxyhypusine synthase holoenzyme in its high ionic strength, low... -

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Basic information

Entry
Database: PDB / ID: 1rlz
TitleDeoxyhypusine synthase holoenzyme in its high ionic strength, low pH crystal form
ComponentsDeoxyhypusine synthase
KeywordsTRANSFERASE / Rossmann Fold / NAD cofactor / deoxyhypusine / hypusine / spermidine
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 / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsUmland, T.C. / Wolff, E.C. / Park, M.-H. / Davies, D.R.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme-NAD-Inhibitor Ternary Complex
Authors: Umland, T.C. / Wolff, E.C. / Park, M.-H. / Davies, D.R.
#1: Journal: 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
DepositionNov 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Aug 23, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,6762
Polymers41,0121
Non-polymers6631
Water2,486138
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)166,7038
Polymers164,0504
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 area33120 Å2
ΔGint-204 kcal/mol
Surface area41190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.600, 108.600, 69.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the crystallographic operations: -y, -x, 69.83-z; -x, -y, z; and y, x, 69.83-z

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Components

#1: Protein Deoxyhypusine synthase / / DHS


Mass: 41012.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Plasmid: pET-11a / 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.: 138 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.7M sodium/potassium phosphate, 100mM Hepes (pH 7.5), NAD, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 30, 1998 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 24976 / Num. obs: 22384 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 4.66 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.058 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.35 % / Num. unique all: 1104 / Rsym value: 0.174 / % possible all: 67.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1DHS

1dhs


Resolution: 2.15→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1295 -random
Rwork0.199 ---
obs0.204 22019 88.2 %-
all-22384 --
Displacement parametersBiso mean: 17.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 44 138 2859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 2.15→2.23 Å / Rfactor Rfree error: 0.007
RfactorNum. reflection% reflection
Rfree0.257 170 -
Rwork0.224 --
obs-2686 65.7 %

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