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- PDB-5c88: Crystal structure of Ard1 N-terminal acetyltransferase from Sulfo... -

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Basic information

Entry
Database: PDB / ID: 5c88
TitleCrystal structure of Ard1 N-terminal acetyltransferase from Sulfolobus solfataricus in monoclinic form
ComponentsUncharacterized N-acetyltransferase SSO0209
KeywordsTRANSFERASE / Acetyltransferase
Function / homology
Function and homology information


N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / NatA complex / protein N-terminal-serine acetyltransferase activity / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / metal ion binding
Similarity search - Function
N-acetyltransferase RimI/Ard1 / 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 / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / N-alpha-acetyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus strain P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChang, Y.Y. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology103-2113-M-002 -009 -MY2 Taiwan
Citation
Journal: Chembiochem / Year: 2016
Title: Multiple Conformations of the Loop Region Confers Heat-Resistance on SsArd1, a Thermophilic NatA.
Authors: Chang, Y.Y. / Hsu, C.H.
#1: Journal: SCI REP / Year: 2015
Title: Structural Basis for Substrate-specific Acetylation of Nalpha-acetyltransferase Ard1 from Sulfolobus solfataricus
Authors: Chang, Y.Y. / Hsu, C.H.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized N-acetyltransferase SSO0209
B: Uncharacterized N-acetyltransferase SSO0209
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1404
Polymers40,6052
Non-polymers1,5352
Water54030
1
A: Uncharacterized N-acetyltransferase SSO0209
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0702
Polymers20,3021
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint0 kcal/mol
Surface area8110 Å2
MethodPISA
2
B: Uncharacterized N-acetyltransferase SSO0209
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0702
Polymers20,3021
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-2 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.154, 84.246, 49.165
Angle α, β, γ (deg.)90.000, 89.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized N-acetyltransferase SSO0209 / Nalpha-acetyltransferase


Mass: 20302.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus strain P2 (archaea)
Strain: P2 / Gene: SSO0209
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q980R9, EC: 2.3.1.88
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.74 Å3/Da / Density % sol: 29.39 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.6 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.2, 0.1 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→30 Å / Num. obs: 9431 / % possible obs: 95.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.087 / Χ2: 1.077 / Net I/av σ(I): 11.436 / Net I/σ(I): 10.3 / Num. measured all: 31094
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.49-2.583.20.4939651.08598.8
2.58-2.683.50.3949581.06799
2.68-2.83.60.3439821.09899.5
2.8-2.953.60.2539651.09998.3
2.95-3.143.60.1939821.09697.6
3.14-3.383.40.1219461.04496.9
3.38-3.723.20.0839311.09695.1
3.72-4.2530.0629131.05892.1
4.25-5.362.80.0488761.08488.8
5.36-302.90.0449131.02589.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3K

4r3k


Resolution: 2.49→26.637 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 893 9.99 %
Rwork0.1608 8046 -
obs0.1714 8939 90.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.76 Å2 / Biso mean: 48.8739 Å2 / Biso min: 25.04 Å2
Refinement stepCycle: final / Resolution: 2.49→26.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 96 30 2718
Biso mean--62.01 51.55 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082751
X-RAY DIFFRACTIONf_angle_d1.1593733
X-RAY DIFFRACTIONf_chiral_restr0.045401
X-RAY DIFFRACTIONf_plane_restr0.004458
X-RAY DIFFRACTIONf_dihedral_angle_d15.851017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4813-2.63660.41381440.24751242138684
2.6366-2.840.33421390.211341148091
2.84-3.12540.28351510.18721386153793
3.1254-3.57670.31251530.15591384153794
3.5767-4.50270.20661520.13541354150691
4.5027-26.63860.24581540.14431339149388
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)
10.3818-0.2681-0.02180.1874-0.16490.40990.0388-0.0001-0.0473-0.2352-0.08140.13460.39150.02270.00020.4562-0.01890.0080.3975-0.02560.4683-31.8745-107.1554-34.5386
20.5936-0.7076-0.05530.98060.34290.97980.1086-0.15190.03820.1977-0.00680.0322-0.00810.13240.00020.3364-0.02110.00850.31510.00990.3342-28.1739-97.6837-26.3309
30.7387-0.2021-0.42680.18340.05630.67780.0419-0.28510.14320.09180.0068-0.0044-0.1876-0.021500.36730.02550.00020.28820.00650.3618-35.0948-87.8412-25.3086
40.555-0.23750.43460.2768-0.28270.40940.20640.19250.1352-0.1138-0.1239-0.1532-0.2850.04230.00010.4174-0.03250.04770.46370.01720.3984-19.6604-105.6318-59.1782
51.1862-0.78670.09890.9020.0870.37230.0116-0.06090.04870.02480.00840.0203-0.0373-0.0718-00.3158-0.0229-0.02560.3595-0.02340.2758-23.2504-113.7892-50.6012
60.14230.03650.02350.37780.0088-0.00830.37980.69390.1017-0.3325-0.0001-0.12980.1587-0.24850.00330.3583-0.0207-0.04850.4918-0.01310.3336-23.1336-120.9245-52.0365
70.5-0.21180.54620.0833-0.21610.577-0.0473-0.3721-0.2806-0.04550.00010.0545-0.00460.16130.00020.4069-0.02370.02770.37170.03250.4043-15.7063-124.9604-50.1582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 48 )A11 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 132 )A49 - 132
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 168 )A133 - 168
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 48 )B11 - 48
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 117 )B49 - 117
6X-RAY DIFFRACTION6chain 'B' and (resid 118 through 132 )B118 - 132
7X-RAY DIFFRACTION7chain 'B' and (resid 133 through 167 )B133 - 167

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