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- PDB-7oju: Chaetomium thermophilum Naa50 GNAT-domain in complex with bisubst... -

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Basic information

Entry
Database: PDB / ID: 7oju
TitleChaetomium thermophilum Naa50 GNAT-domain in complex with bisubstrate analogue CoA-Ac-MVNAL
Components
  • MVNAL Peptide
  • N-acetyltransferase-like protein
KeywordsTRANSFERASE / N-alpha-acetyltransferase / GNAT-fold / Naa50 / Chaetomium thermophilum
Function / homologyN-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / CARBOXYMETHYL COENZYME *A / N-acetyltransferase-like protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsWeidenhausen, J. / Kopp, J. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586/6-1 Germany
German Research Foundation (DFG)201348542 - SFB 1036(TP22) Germany
CitationJournal: Int J Mol Sci / Year: 2022
Title: Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity.
Authors: Weidenhausen, J. / Kopp, J. / Ruger-Herreros, C. / Stein, F. / Haberkant, P. / Lapouge, K. / Sinning, I.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase-like protein
H: MVNAL Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8479
Polymers24,2792
Non-polymers1,5687
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.936, 43.649, 140.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AH

#1: Protein N-acetyltransferase-like protein


Mass: 23732.049 Da / Num. of mol.: 1 / Mutation: N-terminal 81 aa & C-terminal 156 aa deletions
Source method: isolated from a genetically manipulated source
Details: Numbering is wrong: The protein was cloned with N- (81 aa) and C-terminal (156 aa) deletions. Therefore, the first leucine in the cloned sequence corresponds to residue number 82 (and not 3). ...Details: Numbering is wrong: The protein was cloned with N- (81 aa) and C-terminal (156 aa) deletions. Therefore, the first leucine in the cloned sequence corresponds to residue number 82 (and not 3). The N-terminal MG are due to cloning. Hexahistidine at the C-terminus is a His-tag.
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0014970 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0S1V5
#2: Protein/peptide MVNAL Peptide


Mass: 546.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 230 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 62 mg mL-1 protein mixed 1:2 with CoA-Ac-Lys; drops (600 nL): 1:1 mix of (20 mM HEPES pH 7.5, 500 mM NaCl) and (0.1 MES pH 6.0, 8 % (w/v) PEG3000, 37 % (v/v) PEG400). Crystals appeared after ...Details: 62 mg mL-1 protein mixed 1:2 with CoA-Ac-Lys; drops (600 nL): 1:1 mix of (20 mM HEPES pH 7.5, 500 mM NaCl) and (0.1 MES pH 6.0, 8 % (w/v) PEG3000, 37 % (v/v) PEG400). Crystals appeared after 1-2 days; 20 % (v/v) glycerol as cryo protectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976246 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 1.1→41.67 Å / Num. obs: 92854 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 18.01
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 9100 / CC1/2: 0.631 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSversion January 2019data reduction
Aimless7.0.072data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OB0

2ob0


Resolution: 1.1→41.67 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.165 4760 5.13 %
Rwork0.145 88086 -
obs0.146 92846 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.96 Å2 / Biso mean: 21.93 Å2 / Biso min: 7.94 Å2
Refinement stepCycle: final / Resolution: 1.1→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 160 223 2082
Biso mean--39.75 33.11 -
Num. residues----219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.110.28781530.267228883041100
1.11-1.130.23851570.23732873303099
1.13-1.140.24991620.218328673029100
1.14-1.150.21671530.20742904305799
1.15-1.170.23361650.198728733038100
1.17-1.180.2511570.195629173074100
1.18-1.20.20431600.182828743034100
1.2-1.220.21541450.176129293074100
1.22-1.240.19621530.172329183071100
1.24-1.260.17681460.172629013047100
1.26-1.280.20241730.169529253098100
1.28-1.30.19711650.164228873052100
1.3-1.330.16561600.163429153075100
1.33-1.360.18771490.152729223071100
1.36-1.390.16541610.138528953056100
1.39-1.420.15471530.132229453098100
1.42-1.450.16661640.11929123076100
1.45-1.490.16111660.121229133079100
1.49-1.540.14261600.123929343094100
1.54-1.590.13371600.121329343094100
1.59-1.640.16041650.120229183083100
1.64-1.710.13941790.115229183097100
1.71-1.790.14961520.119629903142100
1.79-1.880.14191300.117529533083100
1.88-20.14661730.118329613134100
2-2.150.11651280.119430053133100
2.15-2.370.13811680.12629663134100
2.37-2.710.15951520.139630343186100
2.71-3.420.16451800.145630263206100
3.42-41.670.18131710.172131893360100

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