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- PDB-5cnp: X-ray crystal structure of Spermidine n1-acetyltransferase from V... -

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Basic information

Entry
Database: PDB / ID: 5cnp
TitleX-ray crystal structure of Spermidine n1-acetyltransferase from Vibrio cholerae.
ComponentsSpermidine N(1)-acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / spermidine / spermine / structural genomics / IDP01616 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


polyamine catabolic process / spermidine 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
ISOPROPYL ALCOHOL / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 Å
AuthorsOsipiuk, J. / VOLKART, L. / MOY, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG.
Authors: Filippova, E.V. / Weigand, S. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Anderson, W.F.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionJul 29, 2015ID: 3EG7
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
D: Spermidine N(1)-acetyltransferase
E: Spermidine N(1)-acetyltransferase
F: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,89111
Polymers126,6986
Non-polymers1935
Water4,288238
1
A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
D: Spermidine N(1)-acetyltransferase
E: Spermidine N(1)-acetyltransferase
F: Spermidine N(1)-acetyltransferase
hetero molecules

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
D: Spermidine N(1)-acetyltransferase
E: Spermidine N(1)-acetyltransferase
F: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,78222
Polymers253,39612
Non-polymers38610
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area31540 Å2
ΔGint-106 kcal/mol
Surface area88170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.931, 134.176, 77.477
Angle α, β, γ (deg.)90.000, 114.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Spermidine N(1)-acetyltransferase / SAT / Spermidine/spermine N(1)-acetyltransferase / SSAT


Mass: 21116.330 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: SNA - cloning artifacts
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: speG, VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KL03, diamine N-acetyltransferase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris buffer, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 2004-10-20
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 20, 2004
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: 2.38→38.6 Å / Num. obs: 58601 / % possible obs: 98.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.066 / Χ2: 0.931 / Net I/av σ(I): 20.301 / Net I/σ(I): 10.6 / Num. measured all: 532616
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.473.50.48489010.77191.6
2.47-2.554.30.39596820.77799.7
2.55-2.644.50.30796760.77899.9
2.64-2.754.60.24996860.8199.9
2.75-2.874.70.18997140.846100
2.87-3.024.80.14696810.894100
3.02-3.214.90.197060.978100
3.21-3.464.90.07596471.093100
3.46-3.814.90.06297051.03399.9
3.81-4.364.80.04897010.99599.9
4.36-5.494.70.04196881.02299.8
5.49-404.60.03695961.07299

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.38→36.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.078 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 3934 6.7 %RANDOM
Rwork0.1847 ---
obs0.1881 54667 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.12 Å2 / Biso mean: 50.164 Å2 / Biso min: 25.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.24 Å2
2--0.42 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 2.38→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8657 0 11 238 8906
Biso mean--41.73 43.95 -
Num. residues----1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198897
X-RAY DIFFRACTIONr_bond_other_d0.0010.028402
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.94212012
X-RAY DIFFRACTIONr_angle_other_deg0.782319185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14351028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92123.981535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.454151527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1431571
X-RAY DIFFRACTIONr_chiral_restr0.0790.21265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022333
X-RAY DIFFRACTIONr_mcbond_it2.1073.2514103
X-RAY DIFFRACTIONr_mcbond_other2.1073.254102
X-RAY DIFFRACTIONr_mcangle_it3.3064.8635119
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 229 -
Rwork0.28 3304 -
all-3533 -
obs--80.61 %
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)
10.8444-0.18180.88672.5315-1.05522.3555-0.0110.0696-0.1651-0.4456-0.05720.06230.39340.01750.06820.19670.06390.03360.1448-0.00560.138274.050467.564971.9006
20.8776-0.62550.88961.7859-0.05521.24680.01480.08110.0737-0.2334-0.0711-0.1579-0.06650.21790.05630.03860.02210.02130.21680.03980.09784.681999.575375.283
30.9989-0.08030.44011.90980.89550.71270.01530.08340.0351-0.13420.01850.0929-0.0630.1023-0.03370.0421-0.0452-0.03780.0877-0.00130.186766.8359126.684264.8673
42.0013-0.2575-0.50492.04290.79440.3930.09210.31280.0854-0.1423-0.0235-0.1543-0.0776-0.0804-0.06870.10250.0269-0.05480.14630.09070.147936.6638124.046148.375
51.6076-0.6062-0.51631.68070.26550.17190.00590.2586-0.0074-0.2074-0.0161-0.0596-0.0145-0.09810.01020.076-0.0399-0.03560.2469-0.02780.05922.894694.300940.3566
61.81440.2334-0.45021.7892-0.03360.17710.03840.0897-0.19230.1112-0.1149-0.31080.07810.02590.07650.14060.059-0.04780.1845-0.05020.17238.041164.368546.0879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 173
2X-RAY DIFFRACTION2B2 - 172
3X-RAY DIFFRACTION3C1 - 171
4X-RAY DIFFRACTION4D-1 - 173
5X-RAY DIFFRACTION5E2 - 170
6X-RAY DIFFRACTION6F2 - 170

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