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- PDB-7cmc: CRYSTAL STRUCTURE OF DEOXYHYPUSINE SYNTHASE FROM PYROCOCCUS HORIKOSHII -

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Basic information

Entry
Database: PDB / ID: 7cmc
TitleCRYSTAL STRUCTURE OF DEOXYHYPUSINE SYNTHASE FROM PYROCOCCUS HORIKOSHII
ComponentsProbable deoxyhypusine synthase
KeywordsTRANSFERASE / deoxyhypusine synthase / IF5A / NAD+
Function / homology
Function and homology information


deoxyhypusine synthase / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity
Similarity search - Function
Deoxyhypusine synthase, putative, archaeal / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Probable deoxyhypusine synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYu, J. / Gai, Z.Q. / Okada, C. / Yao, M.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Flexible NAD+Binding in Deoxyhypusine Synthase Reflects the Dynamic Hypusine Modification of Translation Factor IF5A.
Authors: Chen, M. / Gai, Z. / Okada, C. / Ye, Y. / Yu, J. / Yao, M.
History
DepositionJul 27, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 2, 2020ID: 4P63
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Probable deoxyhypusine synthase
B: Probable deoxyhypusine synthase
C: Probable deoxyhypusine synthase
D: Probable deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5796
Polymers156,2524
Non-polymers1,3272
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20920 Å2
ΔGint-152 kcal/mol
Surface area42060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.280, 89.906, 164.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Probable deoxyhypusine synthase / DHS


Mass: 39063.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: dys, PH1397 / Production host: Escherichia coli (E. coli) / References: UniProt: O50105, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 100 mM Phosphate-citrate pH4.8, 32% ethanol, 5% PEG 1000
PH range: 4.2-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 66513 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 29.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.479 / Num. unique obs: 6550

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DHS

1dhs


Resolution: 2.2→35.44 Å / SU ML: 0.2171 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 3322 4.99 %
Rwork0.1752 63191 -
obs0.1779 66513 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.75 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9817 0 88 408 10313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006610126
X-RAY DIFFRACTIONf_angle_d0.931513690
X-RAY DIFFRACTIONf_chiral_restr0.0641502
X-RAY DIFFRACTIONf_plane_restr0.0051713
X-RAY DIFFRACTIONf_dihedral_angle_d19.75633816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.24961460.19792593X-RAY DIFFRACTION99.89
2.23-2.260.27861480.22561X-RAY DIFFRACTION100
2.26-2.30.29971460.20332623X-RAY DIFFRACTION100
2.3-2.340.25021380.2022563X-RAY DIFFRACTION99.96
2.34-2.380.33741480.20312605X-RAY DIFFRACTION99.96
2.38-2.420.31471440.19892602X-RAY DIFFRACTION99.96
2.42-2.470.23361280.18792590X-RAY DIFFRACTION99.96
2.47-2.520.25891410.18672622X-RAY DIFFRACTION100
2.52-2.570.25931310.18082612X-RAY DIFFRACTION100
2.57-2.630.21181500.17522584X-RAY DIFFRACTION100
2.63-2.70.22131320.16642621X-RAY DIFFRACTION99.96
2.7-2.770.20631170.16262639X-RAY DIFFRACTION99.93
2.77-2.850.23761430.16212607X-RAY DIFFRACTION100
2.85-2.950.19661150.16422645X-RAY DIFFRACTION100
2.95-3.050.21511420.16382616X-RAY DIFFRACTION100
3.05-3.170.24281180.17722642X-RAY DIFFRACTION100
3.17-3.320.24981350.18122638X-RAY DIFFRACTION100
3.32-3.490.22261410.17162655X-RAY DIFFRACTION99.96
3.49-3.710.20671430.16892626X-RAY DIFFRACTION100
3.71-40.24511420.16562662X-RAY DIFFRACTION100
4-4.40.18691130.15172687X-RAY DIFFRACTION100
4.4-5.030.21021500.15272676X-RAY DIFFRACTION99.93
5.03-6.330.20811600.19072698X-RAY DIFFRACTION100
6.33-35.440.23161510.19492824X-RAY DIFFRACTION99.66

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