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- PDB-4ncz: Spermidine N-acetyltransferase from Vibrio cholerae in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4ncz
TitleSpermidine N-acetyltransferase from Vibrio cholerae in complex with 2-[n-cyclohexylamino]ethane sulfonate.
ComponentsSpermidine n1-acetyltransferase
KeywordsTRANSFERASE / Structural genomics / spermidine N1-acetyltransferase / IDP01616 / 2-[n-cyclohexylamino]ethane sulfonate / CHES / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
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
Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsOsipiuk, J. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Mol.Biol. / Year: 2015
Title: A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure.
Authors: Filippova, E.V. / Kuhn, M.L. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Ballicora, M.A. / Anderson, W.F.
History
DepositionOct 25, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionNov 6, 2013ID: 4K4L
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)64,50415
Polymers63,3493
Non-polymers1,15512
Water4,972276
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)258,01760
Polymers253,39612
Non-polymers4,62148
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area43100 Å2
ΔGint-526 kcal/mol
Surface area81640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.751, 134.498, 137.086
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
11B-304-

CA

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Spermidine n1-acetyltransferase


Mass: 21116.330 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KL03

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Non-polymers , 5 types, 288 molecules

#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 52.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.2 M lithium sulfate, 0.1 M CHES buffer, 1 M potassium/sodium tartrate, 0.02 M acetylcholine, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 16, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→32.02 Å / Num. all: 52181 / Num. obs: 52181 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.89-1.936.40.5992.76194.7
1.93-1.976.90.537197.7
1.97-2.0170.455196.4
2.01-2.057.10.319197.3
2.05-2.097.30.298198.2
2.09-2.147.50.266197.7
2.14-2.197.60.245198.1
2.19-2.257.80.199198.4
2.25-2.327.90.183198.7
2.32-2.398.10.168199
2.39-2.488.20.147198.9
2.48-2.588.30.129199
2.58-2.78.30.105199.3
2.7-2.848.20.091199.4
2.84-3.028.10.081199.1
3.02-3.2580.071199.5
3.25-3.587.70.062199.5
3.58-4.097.50.054199.5
4.09-5.166.90.048199.6
5.16-5070.046195.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EG7

3eg7
PDB Unreleased entry


Resolution: 1.89→32.02 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 7.153 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23762 2646 5.1 %RANDOM
Rwork0.19072 ---
obs0.19304 49481 97.56 %-
all-52127 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.139 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å20 Å20 Å2
2---4.51 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.89→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 64 276 4648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194579
X-RAY DIFFRACTIONr_bond_other_d0.0010.024328
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9536202
X-RAY DIFFRACTIONr_angle_other_deg0.84939900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45123.692279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21715791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6781542
X-RAY DIFFRACTIONr_chiral_restr0.1050.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021212
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 146 -
Rwork0.278 3285 -
obs--87.59 %
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)
10.2024-0.1146-0.13990.62430.12470.3596-0.00110.03190.00470.0089-0.01820.0882-0.0397-0.00210.01930.0073-0.01520.00380.2377-0.0150.188521.898153.014137.4857
20.24320.34130.07050.48190.0720.585-0.0130.0047-0.0768-0.02580.0158-0.11750.03490.0775-0.00280.0110.02230.03020.263-0.00240.168549.857333.233171.6442
30.40670.21510.28680.3241-0.26041.0145-0.01930.0435-0.0321-0.0113-0.0365-0.047-0.01050.12380.05580.00620.00670.02960.257-0.00690.171849.645247.315540.6707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 171
2X-RAY DIFFRACTION1A301 - 304
3X-RAY DIFFRACTION2B2 - 170
4X-RAY DIFFRACTION2B301 - 305
5X-RAY DIFFRACTION3C4 - 173
6X-RAY DIFFRACTION3C301 - 303

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