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- PDB-4hnw: The NatA Acetyltransferase Complex Bound To Inositol Hexakisphosphate -

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Basic information

Entry
Database: PDB / ID: 4hnw
TitleThe NatA Acetyltransferase Complex Bound To Inositol Hexakisphosphate
Components
  • N-terminal acetyltransferase A complex catalytic subunit ARD1
  • N-terminal acetyltransferase A complex subunit NAT1
KeywordsTRANSFERASE / GNAT/TPR / N-terminal acetyltransferase / inositol hexakisphosphate
Function / homology
Function and homology information


N-terminal protein amino acid propionylation / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / ribosome binding / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Tetratricopeptide repeat ...N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Tetratricopeptide repeat / Aminopeptidase / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / N-terminal acetyltransferase A complex catalytic subunit ARD1 / N-terminal acetyltransferase A complex subunit NAT1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 Å
AuthorsNeubauer, J.L. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Pemble IV, C.W. / York, J.D.
CitationJournal: To be Published
Title: The Protein Complex NatA Binds Inositol Hexakisphosphate and Exhibits Conformational Flexibility
Authors: Neubauer, J.L. / Pham, T. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Li, S. / Pemble IV, C.W. / York, J.D.
History
DepositionOct 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.2Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details ..._chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 28, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-terminal acetyltransferase A complex subunit NAT1
B: N-terminal acetyltransferase A complex catalytic subunit ARD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5878
Polymers128,9562
Non-polymers1,6316
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-24 kcal/mol
Surface area42670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.662, 135.662, 175.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein N-terminal acetyltransferase A complex subunit NAT1 / NatA complex subunit NAT1 / Amino-terminal / alpha-amino / acetyltransferase 1


Mass: 100134.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NAT1, AAA1, YDL040C, D2720 / Plasmid: 22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P12945
#2: Protein N-terminal acetyltransferase A complex catalytic subunit ARD1 / NatA complex subunit ARD1 / Arrest-defective protein 1


Mass: 28821.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ARD1, YHR013C / Plasmid: 30b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P07347, EC: 2.3.1.88
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 0.1 M sodium acetate pH 4.9, 0.175 M ammonium acetate, 3-5% PEG4000, 0.5-4% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM10.97937
SYNCHROTRONAPS 22-BM21
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJul 9, 2010
MARMOSAIC 225 mm CCD2CCDNov 4, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
211
ReflectionResolution: 2.8→50 Å / Num. obs: 46561 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 15.7 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.801→41.487 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 2350 5.05 %random
Rwork0.2288 ---
obs0.23 46492 99.86 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.943 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6716 Å2-0 Å20 Å2
2---3.6716 Å2-0 Å2
3---7.3433 Å2
Refinement stepCycle: LAST / Resolution: 2.801→41.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7322 0 101 85 7508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027569
X-RAY DIFFRACTIONf_angle_d0.6410282
X-RAY DIFFRACTIONf_dihedral_angle_d14.8952706
X-RAY DIFFRACTIONf_chiral_restr0.061149
X-RAY DIFFRACTIONf_plane_restr0.0021328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.85810.40521430.39722543X-RAY DIFFRACTION100
2.8581-2.92020.32241390.31662567X-RAY DIFFRACTION100
2.9202-2.98810.26911290.27012567X-RAY DIFFRACTION100
2.9881-3.06280.30771520.24862548X-RAY DIFFRACTION100
3.0628-3.14560.26691400.25282577X-RAY DIFFRACTION100
3.1456-3.23810.27181310.24722566X-RAY DIFFRACTION100
3.2381-3.34260.23481070.23452596X-RAY DIFFRACTION100
3.3426-3.4620.26861370.23092610X-RAY DIFFRACTION100
3.462-3.60060.26521300.22182562X-RAY DIFFRACTION100
3.6006-3.76430.23721350.21762615X-RAY DIFFRACTION100
3.7643-3.96260.25151500.21392566X-RAY DIFFRACTION100
3.9626-4.21070.2291460.2062583X-RAY DIFFRACTION100
4.2107-4.53540.21291400.19082625X-RAY DIFFRACTION100
4.5354-4.99120.23051340.19392598X-RAY DIFFRACTION100
4.9912-5.71180.25681410.24862646X-RAY DIFFRACTION100
5.7118-7.19020.26411430.26092650X-RAY DIFFRACTION100
7.1902-41.49170.22981530.21562723X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.18190.5789-0.04242.74890.48292.26240.12090.55670.1054-0.6732-0.2175-0.0298-0.1594-0.27230.08040.6975-0.0611-0.06230.62310.13470.373631.022-34.636-33.1458
20.72610.27670.36320.72680.14450.6560.0211-0.2133-0.06950.1355-0.0145-0.05750.19120.06530.00530.5669-0.3477-0.10220.33620.08630.155957.108-38.06578.4174
30.52430.81460.08262.8950.5620.974-0.0740.02870.2727-0.2698-0.03830.4258-0.1618-0.09390.1410.5387-0.2448-0.17140.34150.05640.370344.0084-17.5345-4.52
41.36220.2716-0.47541.68170.09361.31850.00170.27240.4225-0.5462-0.00020.6801-0.4903-0.12270.0830.6787-0.2127-0.26090.37790.09890.520439.4782-4.9782-13.5712
50.3282-0.80230.30013.10050.44321.69720.0007-0.4014-0.05510.1545-0.04580.79650.1663-0.56340.08130.6005-0.27750.09890.7023-0.10680.829926.4602-20.550113.9989
64.30260.7471-0.39640.90050.67411.7279-0.23330.0726-0.23490.34530.05780.6189-0.6420.07860.16121.0138-0.20280.22090.7471-0.09660.861739.5221-4.966819.3568
71.5509-0.32280.73331.1688-0.50630.8701-0.0267-0.10930.0419-0.0749-0.0172-0.0761-0.0130.0190.01480.5972-0.2671-0.07630.33020.0660.223756.3779-35.263-0.7132
82.3277-0.55860.47391.7017-0.96510.5591-0.2013-0.49820.06790.46760.19530.09020.0591-0.01270.03880.6608-0.2573-0.06620.44090.06870.283555.1808-31.88026.7999
97.5872-1.6991-3.81264.80681.57832.03450.08711.2838-0.4603-0.8726-0.6467-0.7432-0.91850.33630.45590.7763-0.072-0.13180.9336-0.00180.50862.657-49.3692-19.6693
101.1541-0.2321-0.26872.1033-0.15792.899-0.09730.14180.0821-0.21340.1219-0.2956-0.20340.40380.13810.5003-0.257-0.04210.48280.08080.238667.6154-39.01370.4975
111.24920.0608-0.80781.7041-1.11421.7959-0.20510.14980.187-0.95210.2162-0.1814-0.09420.5590.05960.7921-0.29470.02470.68530.00270.350774.4633-36.8755-10.1613
125.6698-0.62531.79483.5019-1.97884.66640.024-0.8817-0.79090.51150.1412-0.47080.46680.9015-0.10740.7794-0.1716-0.15320.7406-0.01680.627769.7629-57.395118.83
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 15:119)
2X-RAY DIFFRACTION2chain 'A' and (resseq 120:477)
3X-RAY DIFFRACTION3chain 'A' and (resseq 478:624)
4X-RAY DIFFRACTION4chain 'A' and (resseq 625:698)
5X-RAY DIFFRACTION5chain 'A' and (resseq 699:778)
6X-RAY DIFFRACTION6chain 'A' and (resseq 779:856)
7X-RAY DIFFRACTION7chain 'B' and (resseq 2:54)
8X-RAY DIFFRACTION8chain 'B' and (resseq 55:100)
9X-RAY DIFFRACTION9chain 'B' and (resseq 101:111)
10X-RAY DIFFRACTION10chain 'B' and (resseq 112:144)
11X-RAY DIFFRACTION11chain 'B' and (resseq 145:193)
12X-RAY DIFFRACTION12chain 'B' and (resseq 194:227)

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