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- PDB-4mj8: Crystal structure of spermidine N-acetyltransferase from Vibrio c... -

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Basic information

Entry
Database: PDB / ID: 4mj8
TitleCrystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with polyamine
ComponentsSpermidine n1-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / spermidine / N-acetyltransferase
Function / homology
Function and homology information


polyamine catabolic process / spermine catabolic process / spermidine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
ETHANOL / SPERMINE / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Kuhn, M.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with polyamine
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Kuhn, M.L. / Anderson, W.F.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Structure summary
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,01313
Polymers62,9273
Non-polymers1,08610
Water5,657314
1
A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,05152
Polymers251,70812
Non-polymers4,34340
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area46170 Å2
ΔGint87 kcal/mol
Surface area80290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.999, 135.445, 141.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-392-

HOH

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Components

#1: Protein Spermidine n1-acetyltransferase


Mass: 20975.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9KL03
#2: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris HCl, 20% Ethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2011 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. all: 45842 / Num. obs: 45842 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 49.3
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 9 / Num. unique all: 2180 / % possible all: 96.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EG7

3eg7
PDB Unreleased entry


Resolution: 2.04→29.77 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.533 / SU ML: 0.107 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21087 2320 5.1 %RANDOM
Rwork0.16931 ---
obs0.17141 43518 99.02 %-
all-43518 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.192 Å2
Baniso -1Baniso -2Baniso -3
1-5.53 Å20 Å20 Å2
2---4.24 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.04→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 74 314 4688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194569
X-RAY DIFFRACTIONr_bond_other_d0.0010.024375
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9446148
X-RAY DIFFRACTIONr_angle_other_deg0.86739987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4395523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33123.869274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7315794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6581538
X-RAY DIFFRACTIONr_chiral_restr0.1220.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021223
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_it2.9882.9492074
X-RAY DIFFRACTIONr_mcbond_other2.9882.9492073
X-RAY DIFFRACTIONr_mcangle_it3.824.3972603
X-RAY DIFFRACTIONr_mcangle_other3.824.3972604
X-RAY DIFFRACTIONr_scbond_it4.0723.3932495
X-RAY DIFFRACTIONr_scbond_other4.0713.3952496
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6134.9273546
X-RAY DIFFRACTIONr_long_range_B_refined7.56713.9835413
X-RAY DIFFRACTIONr_long_range_B_other7.54613.8015292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 147 -
Rwork0.232 2911 -
obs--90.21 %
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)
10.39410.30930.2621.0321-0.0911.43410.0507-0.04580.07430.44850.03750.334-0.1754-0.2306-0.08820.22140.04260.15250.04830.01520.116-14.1909-53.271131.738
20.2091-0.5976-0.151.9335-0.09491.62760.0563-0.03250.137-0.0488-0.0588-0.3962-0.40210.45170.00250.1022-0.11050.0150.12580.00840.119114.2017-33.2553-3.1754
30.1532-0.3416-0.331.64770.34250.9167-0.0001-0.08870.06460.3485-0.011-0.4251-0.15550.27260.01110.1596-0.0768-0.10250.10540.02160.140714.1937-47.479328.2956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 171
2X-RAY DIFFRACTION2B3 - 170
3X-RAY DIFFRACTION3C4 - 173

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