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- PDB-6zmp: Crystal structure of Chaetomium thermophilum Naa20 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6zmp
TitleCrystal structure of Chaetomium thermophilum Naa20 in complex with a bisubstrate analogue
Components
  • CMC-MET-ASP-GLU-LEU
  • N-terminal acetyltransferase-like protein
KeywordsCYTOSOLIC PROTEIN / N-terminal acetyltransferase / GNAT / catalytic subunit
Function / homologyN-acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / CARBOXYMETHYL COENZYME *A / N-terminal acetyltransferase-like protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsLayer, D. / Kopp, J. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)Collaborative Research centre 1036 Germany
Other privateLeibniz Programme Germany
CitationJournal: Commun Biol / Year: 2021
Title: Structural basis of Naa20 activity towards a canonical NatB substrate.
Authors: Layer, D. / Kopp, J. / Fontanillo, M. / Kohn, M. / Lapouge, K. / Sinning, I.
History
DepositionJul 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-terminal acetyltransferase-like protein
B: N-terminal acetyltransferase-like protein
C: CMC-MET-ASP-GLU-LEU
D: CMC-MET-ASP-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6206
Polymers46,9694
Non-polymers1,6512
Water10,395577
1
A: N-terminal acetyltransferase-like protein
C: CMC-MET-ASP-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3103
Polymers23,4842
Non-polymers8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-5 kcal/mol
Surface area9970 Å2
MethodPISA
2
B: N-terminal acetyltransferase-like protein
D: CMC-MET-ASP-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3103
Polymers23,4842
Non-polymers8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-3 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.150, 114.453, 47.416
Angle α, β, γ (deg.)90.000, 90.190, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 2 - 191 / Label seq-ID: 2 - 191

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein N-terminal acetyltransferase-like protein


Mass: 22977.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0066240 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGG4
#2: Protein/peptide CMC-MET-ASP-GLU-LEU


Mass: 506.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: CtNaa20 was concentrated to 20 mg/ml and mixed in a 1:3 molar ratio with CoA-Ac-MDEL. The crystallization drops contained 200 nl protein solution and 200 nl precipitant solution (15 % (v/v) ...Details: CtNaa20 was concentrated to 20 mg/ml and mixed in a 1:3 molar ratio with CoA-Ac-MDEL. The crystallization drops contained 200 nl protein solution and 200 nl precipitant solution (15 % (v/v) propanol, 0.2 M ammonium acetate and 0.1 M TRIS pH 8.5).

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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: P14 (MX2) / Wavelength: 0.976247 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 1.57→47.42 Å / Num. obs: 67562 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.056 / Net I/σ(I): 8.6
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.306 / Num. unique obs: 3320 / CC1/2: 0.605 / Rpim(I) all: 0.817 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k18

5k18


Resolution: 1.57→47.42 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 3321 5.11 %
Rwork0.1713 61697 -
obs0.1731 65018 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.85 Å2 / Biso mean: 30.9085 Å2 / Biso min: 13.49 Å2
Refinement stepCycle: final / Resolution: 1.57→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 296 577 4001
Biso mean--31.37 40.6 -
Num. residues----380
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1898X-RAY DIFFRACTION4.487TORSIONAL
12B1898X-RAY DIFFRACTION4.487TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.590.30311660.29872641280798
1.59-1.620.29071170.26372649276698
1.62-1.640.24151600.23962657281799
1.64-1.670.29321510.22972640279199
1.67-1.70.22761400.22127472887100
1.7-1.730.26231140.21332668278299
1.73-1.760.26691780.20462675285399
1.76-1.80.20281310.19012652278399
1.8-1.840.19481270.18512745287299
1.84-1.880.22021820.18832603278599
1.88-1.930.4517970.32891546164358
1.93-1.980.29741400.25282123226380
1.98-2.040.22251570.17972653281099
2.04-2.10.24391260.17422687281399
2.1-2.180.1891300.17042677280799
2.18-2.260.3994770.24941922199970
2.26-2.370.2081270.18672521264893
2.37-2.490.20951220.16582710283299
2.49-2.650.2161340.169527172851100
2.65-2.850.18691750.16826652840100
2.85-3.140.18271160.161327482864100
3.14-3.590.1771470.14152680282799
3.59-4.530.1721500.13562631278197
4.53-47.420.15471570.14212740289799
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)
14.2703-1.1459-0.22533.1650.53973.61570.08010.23780.2873-0.3101-0.10320.0371-0.1599-0.1646-0.01860.240.0144-0.03080.2565-0.00720.2457-33.52028.4721-1.9007
23.0482-2.5491-2.91972.94481.72223.4345-0.07760.1307-0.3875-0.1634-0.05390.4511-0.0348-0.25920.14410.1720.0046-0.03490.29940.00410.2569-35.66-2.5666-2.4641
33.0339-0.2401-1.20463.756-1.77656.08520.06580.05220.2217-0.0242-0.02090.0592-0.4625-0.0483-0.04930.14480.0195-0.04080.1893-0.00420.1731-31.9675.4733.6851
42.0461-0.3391.06978.94970.32111.0002-0.09820.0808-0.26540.07190.1350.57940.3313-0.1791-0.03180.2345-0.02330.06360.22390.01030.2802-37.0016-20.061814.4803
51.4810.4854-0.59170.9616-0.31631.33590.00750.01480.08280.02830.0120.0751-0.06070.0396-0.01170.1060.0121-0.01140.1618-0.00740.1375-25.1041-2.18257.7288
62.06640.66940.14122.9121-0.22641.006-0.1190.342-0.1751-0.47050.128-0.03550.19070.27070.01270.24720.00940.01510.2302-0.00980.1938-21.2295-12.89961.381
73.5523-1.4265-1.33624.85763.21496.7080.0651-0.2135-0.29850.0565-0.0239-0.12210.36080.4965-0.05140.20190.0515-0.03240.23620.03080.2521-23.0726-14.39420.4093
83.2354-2.55053.49755.5143-1.45014.852-0.25950.24640.3164-0.07570.0512-0.12010.4672-0.3460.06280.29240.00320.01020.348-0.01330.271-27.4489-21.7075.2026
92.9165-0.7469-0.25142.7752-0.4263.58940.00860.239-0.263-0.2492-0.0394-0.11010.12940.09440.05010.20450.01550.00560.24540.00860.2385-1.4242-6.703921.8614
108.3933-2.71552.52243.1071-1.6664.1471-0.02470.32380.2789-0.0203-0.098-0.3787-0.09250.2370.17510.1746-0.0020.02590.2031-0.02070.23980.71264.285821.3595
113.41870.02921.37484.08682.23995.67510.1365-0.0223-0.21740.0725-0.0506-0.13950.4411-0.0232-0.11630.16390.02440.00220.21910.01150.1854-2.9841-3.679427.4399
122.67530.1125-1.56240.423-0.61881.6449-0.0695-0.06180.67070.525-0.2457-1.1128-0.67460.3650.15060.319-0.048-0.11470.2887-0.00730.41921.726921.860138.3158
131.02250.34320.44871.18760.37441.06850.0127-0.0671-0.02530.021-0.0091-0.08350.0594-0.0259-0.01140.14790.01160.0010.20970.00930.1774-9.94613.959231.4567
142.06780.7350.08032.79720.09910.683-0.10040.34320.1586-0.47850.11440.0103-0.1168-0.1106-0.03630.22980.015-0.00840.23930.01620.1792-13.83214.629425.068
150.9268-0.52470.20012.9127-2.35984.58060.056-0.03520.08630.1480.0110.0697-0.39940.0632-0.17140.2240.00970.00140.233-0.03030.2336-9.969119.731736.967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )A2 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 38 )A21 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 62 )A39 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 77 )A63 - 77
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 123 )A78 - 123
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 165 )A124 - 165
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 178 )A166 - 178
8X-RAY DIFFRACTION8chain 'A' and (resid 179 through 191 )A179 - 191
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 20 )B2 - 20
10X-RAY DIFFRACTION10chain 'B' and (resid 21 through 38 )B21 - 38
11X-RAY DIFFRACTION11chain 'B' and (resid 39 through 62 )B39 - 62
12X-RAY DIFFRACTION12chain 'B' and (resid 63 through 77 )B63 - 77
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 123 )B78 - 123
14X-RAY DIFFRACTION14chain 'B' and (resid 124 through 165 )B124 - 165
15X-RAY DIFFRACTION15chain 'B' and (resid 166 through 191 )B166 - 191

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