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- PDB-4mi4: Crystal structure of spermidine N-acetyltransferase from Vibrio c... -

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Basic information

Entry
Database: PDB / ID: 4mi4
TitleCrystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with spermine
ComponentsSpermidine n1-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / spermidine / N-acetyltransferase
Function / homology
Function and homology information


spermidine catabolic process / polyamine catabolic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
SPERMINE / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 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: 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
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Atomic model
Revision 1.2Mar 25, 2015Group: 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

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)70,9496
Polymers70,3423
Non-polymers6073
Water9,854547
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)283,79624
Polymers281,36812
Non-polymers2,42812
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 area40400 Å2
ΔGint25 kcal/mol
Surface area81450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.633, 135.898, 140.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Spermidine n1-acetyltransferase


Mass: 23447.320 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 / Spermine


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M 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-G / Wavelength: 0.987856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2011 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987856 Å / Relative weight: 1
ReflectionResolution: 1.848→30 Å / Num. all: 59130 / Num. obs: 59130 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 38.8
Reflection shellResolution: 1.848→1.88 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.6 / % possible all: 99.8

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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: 1.848→28.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.097 / SU ML: 0.065 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2975 5.1 %RANDOM
Rwork0.14936 ---
obs0.15115 55591 99.23 %-
all-55591 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---1.08 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.848→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 42 547 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194549
X-RAY DIFFRACTIONr_bond_other_d0.0010.024317
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.946141
X-RAY DIFFRACTIONr_angle_other_deg0.89539861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2675525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94523.81273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.17715793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3581538
X-RAY DIFFRACTIONr_chiral_restr0.1360.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025267
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021221
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_it2.6152.0482079
X-RAY DIFFRACTIONr_mcbond_other2.6152.0482078
X-RAY DIFFRACTIONr_mcangle_it3.3423.0512611
X-RAY DIFFRACTIONr_mcangle_other3.3413.0512612
X-RAY DIFFRACTIONr_scbond_it4.1532.4262470
X-RAY DIFFRACTIONr_scbond_other4.1522.4272471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7293.5013531
X-RAY DIFFRACTIONr_long_range_B_refined7.79618.5815590
X-RAY DIFFRACTIONr_long_range_B_other7.62917.5865309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 215 -
Rwork0.175 3829 -
obs--93.01 %
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)
10.16190.0540.05461.56790.1261.6025-0.0451-0.0143-0.0164-0.0540.0803-0.12910.0115-0.0187-0.03520.02720.0049-0.00610.0559-0.02860.064220.5051-53.3998-24.612
20.2775-0.2546-0.04530.24820.14481.04150.0101-0.04320.04020.00570.0489-0.04920.02360.0726-0.05890.0385-0.0031-0.01150.0315-0.00060.081815.0362-57.0552-25.8981
30.42910.01730.07130.54040.08430.1865-0.0250.0122-0.0216-0.11130.0532-0.1091-0.009-0.0292-0.02820.0492-0.01670.03280.031-0.00020.088313.5625-53.4036-40.2783
40.10140.16850.12791.0613-0.29190.5717-0.0665-0.0014-0.0121-0.2630.0494-0.0184-0.03890.05740.01710.0917-0.03010.01320.0880.00760.08467.041-46.5818-38.4048
50.1509-0.1046-0.21560.5831-0.18970.8623-0.01080.0303-0.03030.0067-0.0269-0.0266-0.0543-0.12310.03770.0522-0.00290.00010.0902-0.03030.0458-16.6344-42.8182-0.197
63.18340.0421-0.77450.56360.55930.80.00650.26870.0257-0.0199-0.08180.0615-0.0663-0.18420.07530.06220.0331-0.02350.09360.00880.0664-18.185-33.666.5844
70.19250.1182-0.3440.2493-0.09991.58050.02370.0188-0.02020.0108-0.00390.035-0.1595-0.1871-0.01980.05610.035-0.0190.04780.00560.0652-9.9155-25.33193.1479
80.5655-0.1053-0.27191.94040.75620.39940.16610.04030.0439-0.0764-0.17460.1467-0.1463-0.07530.00850.23540.03190.0070.0364-0.0060.0848-7.4387-23.34814.9503
90.16940.10050.04911.35430.45210.8428-0.036-0.0103-0.01820.0378-0.02590.16640.0066-0.0030.06180.04230.0010.03130.0137-0.00920.0917-16.4329-55.7592-21.7056
102.0449-0.4720.02031.5974-0.09310.079-0.00380.0465-0.1653-0.0006-0.02830.3235-0.0363-0.04650.03210.03370.0072-0.01270.0979-0.02810.1205-18.2531-45.1661-26.2399
110.1321-0.2339-0.08551.05780.29880.22520.0134-0.0185-0.0344-0.0979-0.05670.1013-0.0368-0.07530.04340.04270.0046-0.02340.0684-0.00690.0712-9.1242-44.5118-35.9527
124.2056-6.98520.624115.4444-3.11571.218-0.12150.026-0.0670.05350.12940.13190.0651-0.0859-0.0080.09540.0321-0.0280.0289-0.00030.0857-10.3435-27.1031-30.5488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 96
3X-RAY DIFFRACTION3A97 - 141
4X-RAY DIFFRACTION4A142 - 171
5X-RAY DIFFRACTION5B3 - 59
6X-RAY DIFFRACTION6B60 - 105
7X-RAY DIFFRACTION7B106 - 153
8X-RAY DIFFRACTION8B154 - 170
9X-RAY DIFFRACTION9C4 - 59
10X-RAY DIFFRACTION10C60 - 105
11X-RAY DIFFRACTION11C106 - 165
12X-RAY DIFFRACTION12C166 - 173

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