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- PDB-2jev: Crystal structure of human spermine,spermidine acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 2jev
TitleCrystal structure of human spermine,spermidine acetyltransferase in complex with a bisubstrate analog (N1-acetylspermine-S-CoA).
ComponentsDIAMINE ACETYLTRANSFERASE 1
KeywordsTRANSFERASE / ACYLTRANSFERASE / ACETYLTRANSFERASE / GCN5 RELATED N-ACETYLTRANSFERASE / POLYAMINE BIOSYNTHESIS / GNAT / SPERMINE / SPERMIDINE / BISUBSTRATE
Function / homology
Function and homology information


Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine biosynthetic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / N-acetyltransferase activity / angiogenesis / identical protein binding / cytosol
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NHQ / Diamine acetyltransferase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHegde, S.S. / Chandler, J. / Vetting, M.W. / Yu, M. / Blanchard, J.S.
CitationJournal: Biochemistry / Year: 2007
Title: Mechanistic and Structural Analysis of Human Spermidine/Spermine N(1)-Acetyltransferase.
Authors: Hegde, S.S. / Chandler, J. / Vetting, M.W. / Yu, M. / Blanchard, J.S.
History
DepositionJan 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIAMINE ACETYLTRANSFERASE 1
B: DIAMINE ACETYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6804
Polymers40,6612
Non-polymers2,0202
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.729, 46.729, 191.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein DIAMINE ACETYLTRANSFERASE 1 / SPERMINE SPERMIDINE ACETYLTRANSFERASE / SPERMIDINE/SPERMINE N(1)-ACETYLTRANSFERASE 1 / SSAT / SSAT- ...SPERMINE SPERMIDINE ACETYLTRANSFERASE / SPERMIDINE/SPERMINE N(1)-ACETYLTRANSFERASE 1 / SSAT / SSAT-1 / PUTRESCINE ACETYLTRANSFERASE / POLYAMINE N-ACETYLTRANSFERASE 1


Mass: 20330.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21673, diamine N-acetyltransferase
#2: Chemical ChemComp-NHQ / (3R)-27-AMINO-3-HYDROXY-2,2-DIMETHYL-4,8,14-TRIOXO-12-THIA-5,9,15,19,24-PENTAAZAHEPTACOS-1-YL [(2S,3R,4S,5S)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE / N1-ACETYLSPERMINE-S-COA


Mass: 1009.895 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H62N11O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGSH AT START OF SEQUENCE IS A REMNANT OF THE N-TERMINAL THROMBIN CLEAVED 6XHIS-TAG USED IN PURIFICATION.

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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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN AT 15MG/ML IN 20 MM TRIS PH 8.0 CONTAINING 1 MM DTT, 0.1 MM EDTA, 4MM N1-ACETYLSPERMINE-S-COA. CRYSTALLIZED BY HANGING DROP VAPOUR DIFFUSION WITH 3-4 M NACL, 200 MM K/NA TARTRATE, ...Details: PROTEIN AT 15MG/ML IN 20 MM TRIS PH 8.0 CONTAINING 1 MM DTT, 0.1 MM EDTA, 4MM N1-ACETYLSPERMINE-S-COA. CRYSTALLIZED BY HANGING DROP VAPOUR DIFFUSION WITH 3-4 M NACL, 200 MM K/NA TARTRATE, 100 MM TRIS-HCL PH 7-8, 50 MM MGCL2

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Data collection

DiffractionMean temperature: 194 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→33.5 Å / Num. obs: 17959 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.3 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F5I

2f5i


Resolution: 2.3→47.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.647 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 908 5.1 %RANDOM
Rwork0.224 ---
obs0.227 16978 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---1.04 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 130 67 2981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9924048
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45423.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33715500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7631516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022236
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21240
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21980
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.51747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44422698
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.58431485
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5524.51350
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 59
Rwork0.27 1200

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