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

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Basic information

Entry
Database: PDB / ID: 4mhd
TitleCrystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with spermidine
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
SPERMIDINE / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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 / 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)70,7786
Polymers70,3423
Non-polymers4363
Water2,306128
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)283,11124
Polymers281,36812
Non-polymers1,74312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area39220 Å2
ΔGint44 kcal/mol
Surface area81210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.453, 136.012, 139.831
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-332-

HOH

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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-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M NaCl, 30% Ethanol, 0.1M Tris HCl, 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 12, 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: 2.3→30 Å / Num. all: 30239 / Num. obs: 30239 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 43.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 7.9 / % possible all: 100

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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: 2.32→29.33 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.659 / SU ML: 0.169 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25377 1522 5 %RANDOM
Rwork0.19561 ---
obs0.19852 28715 97.93 %-
all-28715 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.973 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.32→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 30 128 4480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194506
X-RAY DIFFRACTIONr_bond_other_d0.0010.024262
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9386079
X-RAY DIFFRACTIONr_angle_other_deg0.85939735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4775518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.77423.971272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9215789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5461536
X-RAY DIFFRACTIONr_chiral_restr0.1290.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021198
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_it2.7742.6342066
X-RAY DIFFRACTIONr_mcbond_other2.7732.6332065
X-RAY DIFFRACTIONr_mcangle_it3.7873.9372586
X-RAY DIFFRACTIONr_mcangle_other3.7863.9372587
X-RAY DIFFRACTIONr_scbond_it3.8022.9762440
X-RAY DIFFRACTIONr_scbond_other3.8012.9772441
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2544.3453494
X-RAY DIFFRACTIONr_long_range_B_refined6.82412.1595100
X-RAY DIFFRACTIONr_long_range_B_other6.81612.1195080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.377 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 120 -
Rwork0.264 1886 -
obs--88.49 %
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)
14.9141-0.3283-2.60586.5524-0.86117.99480.0150.1979-0.4715-0.83930.2490.70380.121-0.5478-0.26390.1751-0.0092-0.20320.1870.03720.3523-22.5298-9.533445.8153
20.4573-1.06230.38745.4111-0.21542.73370.1230.0497-0.258-0.6150.11590.35450.404-0.201-0.23890.171-0.023-0.07210.2415-0.01490.2197-14.2091-14.145248.9205
31.84240.85040.30952.8664-0.73081.88310.1105-0.0808-0.007-0.6752-0.02870.49180.1707-0.2644-0.08180.44880.0183-0.20880.1559-0.04350.1371-14.7767-13.161833.786
41.4517-0.24760.31457.6071-4.20675.2933-0.1309-0.0211-0.0611-1.12290.35230.19530.1958-0.5621-0.22150.52740.0038-0.09650.1689-0.06550.1066-6.7538-21.404831.5311
57.6960.0113-0.11832.7746-2.489417.76320.16560.2513-0.8443-0.3717-0.1851-0.47791.56521.35140.01950.16310.0743-0.03390.44110.09630.422222.4128-25.660573.5731
63.23182.78172.24187.8268-9.936327.76910.1324-0.2241-0.4915-0.4233-0.9912-0.86791.07662.06370.85880.33260.0818-0.00390.69690.10450.676615.9478-33.700461.5144
70.27780.77540.23024.3235-1.42692.17490.08020.1114-0.1646-0.0051-0.2431-0.75930.25930.62590.16290.04890.0453-0.02750.35120.01940.244115.4979-28.1673.998
80.7281-0.02180.90732.01481.29886.90680.0873-0.0016-0.21220.1497-0.0254-0.46730.74590.8242-0.06190.09320.1056-0.02280.19960.05320.26310.2533-42.594274.2424
92.6475-0.6372.45154.4432-2.54154.10870.20840.4054-0.1034-0.8165-0.4238-1.32560.48950.4850.21540.20280.08330.22270.23360.03030.576622.2267-14.288347.6917
101.8329-0.85930.87513.2345-4.08675.2109-0.07560.3414-0.2736-0.3518-0.1987-0.24120.40320.18680.27430.2506-0.01670.19150.1631-0.05060.251414.0486-6.957145.3116
113.38351.82690.99664.4021.1341.458-0.02590.2284-0.2214-0.36440.0519-0.66440.04290.273-0.0260.12210.03010.04740.18610.00770.160112.8858-20.456350.3748
121.041-0.90860.26683.5384-1.07852.51330.03770.06770.1404-0.7676-0.092-0.79850.05340.36680.05430.38040.05990.18190.1803-0.04330.209612.7258-23.642435.89
1310.3552-14.68616.649933.83544.67619.5852-0.1444-0.03220.4709-0.5490.718-1.555-0.88070.705-0.57360.4486-0.01480.3160.1816-0.04410.480111.7968-42.686440.5582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 22
2X-RAY DIFFRACTION2A23 - 62
3X-RAY DIFFRACTION3A63 - 140
4X-RAY DIFFRACTION4A141 - 171
5X-RAY DIFFRACTION5B2 - 23
6X-RAY DIFFRACTION6B24 - 35
7X-RAY DIFFRACTION7B36 - 99
8X-RAY DIFFRACTION8B100 - 170
9X-RAY DIFFRACTION9C2 - 27
10X-RAY DIFFRACTION10C28 - 46
11X-RAY DIFFRACTION11C47 - 83
12X-RAY DIFFRACTION12C84 - 168
13X-RAY DIFFRACTION13C169 - 173

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