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- PDB-5k04: The NatB Acetyltransferase Complex Bound To CoA and MES -

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Basic information

Entry
Database: PDB / ID: 5k04
TitleThe NatB Acetyltransferase Complex Bound To CoA and MES
Components
  • N-terminal acetyltransferase B complex subunit NAT3
  • Uncharacterized protein
KeywordsTRANSFERASE / N-terminal acetyltransferase complex
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
N-acetyltransferase B complex, non-catalytic subunit / N-acetyltransferase B complex (NatB) non catalytic subunit / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
COENZYME A / N-terminal acetyltransferase B complex subunit NAT3 / N-terminal acetyltransferase B complex subunit MDM20
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsHong, H. / Cai, Y. / Zhang, S. / Han, A.
CitationJournal: Structure / Year: 2017
Title: Molecular Basis of Substrate Specific Acetylation by N-Terminal Acetyltransferase NatB
Authors: Hong, H. / Cai, Y. / Zhang, S. / Ding, H. / Wang, H. / Han, A.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein
B: N-terminal acetyltransferase B complex subunit NAT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4234
Polymers107,4602
Non-polymers9632
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-16 kcal/mol
Surface area36910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.450, 108.450, 223.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uncharacterized protein


Mass: 87547.102 Da / Num. of mol.: 1 / Mutation: S256L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain WO-1) (yeast) / Strain: WO-1 / Gene: CAWG_01335 / Plasmid: pET-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C4YFL7
#2: Protein N-terminal acetyltransferase B complex subunit NAT3


Mass: 19912.736 Da / Num. of mol.: 1 / Fragment: UNP residues 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain WO-1) (yeast) / Strain: WO-1 / Gene: CAWG_00748 / Plasmid: pET-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C4YDZ9
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Fragment: CoA / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: PEG600, PEG1000, Glycerol,1,3-butanediol, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.33→25 Å / Num. obs: 57791 / % possible obs: 99.1 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.138 / Χ2: 1.585 / Net I/σ(I): 9.8 / Num. measured all: 616156
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.33-2.379.30.74623391.306182
2.37-2.41100.71428711.308199.9
2.41-2.46100.64628481.336199.9
2.46-2.5110.10.54528571.3531100
2.51-2.5610.10.46628851.3781100
2.56-2.6210.20.42328551.4151100
2.62-2.6910.30.34828871.4481100
2.69-2.7610.30.31728751.5321100
2.76-2.8410.40.27828701.5651100
2.84-2.9310.50.24429001.5911100
2.93-3.0410.60.20328861.7251100
3.04-3.1610.80.16928931.8441100
3.16-3.310.90.14829131.8321100
3.3-3.4811.10.12529121.7711100
3.48-3.711.30.10729201.9071100
3.7-3.9811.40.10129311.4171100
3.98-4.3811.50.10329551.7011100
4.38-5.0111.60.11129782.0821100
5.01-6.2911.40.10730101.6571100
6.29-25110.0832061.283199.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
AutoSolmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→24.817 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1782 3.37 %
Rwork0.1988 51048 -
obs0.2002 52830 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.45 Å2 / Biso mean: 53.9756 Å2 / Biso min: 8.41 Å2
Refinement stepCycle: final / Resolution: 2.4→24.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7180 0 60 331 7571
Biso mean--55.49 37.62 -
Num. residues----885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087381
X-RAY DIFFRACTIONf_angle_d0.8919898
X-RAY DIFFRACTIONf_chiral_restr0.0461135
X-RAY DIFFRACTIONf_plane_restr0.0051240
X-RAY DIFFRACTIONf_dihedral_angle_d12.9784432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.46480.2981990.237539064005
2.4648-2.53730.3168990.21938633962
2.5373-2.61910.25541980.20538104008
2.6191-2.71260.2627990.199439054004
2.7126-2.82110.26381980.201638174015
2.8211-2.94930.2827990.205839194018
2.9493-3.10450.2265990.204439474046
3.1045-3.29860.25541980.205638274025
3.2986-3.55260.2169990.200339454044
3.5526-3.90890.24941980.18538804078
3.9089-4.47160.1888990.170539984097
4.4716-5.6230.2061150.18240514166
5.623-24.81830.23081820.226641804362
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)
11.5461-0.08081.07210.73180.24581.3573-0.0602-0.52570.04580.41850.0381-0.90670.08510.9783-0.04650.5253-0.0033-0.12381.0134-0.00290.6154-0.655312.2073-19.8718
21.2445-0.1324-0.12441.91810.84931.5090.04620.0073-0.0650.0174-0.14580.39690.1104-0.18470.0750.2543-0.0167-0.03670.2705-0.0290.3373-40.62764.4429-41.0375
30.8898-0.41470.20931.0146-0.15510.7076-0.04650.0373-0.0926-0.04350.0077-0.07950.11130.09020.04650.2822-0.04490.05530.2673-0.01230.2643-10.9318-24.2135-40.4612
40.3256-0.5235-0.32451.03050.46830.36010.0262-0.1175-0.0410.0352-0.07230.11450.10720.0329-0.01140.2627-0.0679-0.01770.314-0.00120.2573-26.714-5.6204-47.3161
50.428-0.14190.16371.0393-0.05120.3495-0.0154-0.0103-0.00470.0848-0.02870.2011-0.03590.05320.01410.307-0.07560.01160.27950.00490.2729-23.5734-1.3931-51.6266
63.1625-0.87630.67752.00381.20162.52430.05110.0610.2047-0.2797-0.0471-0.2595-0.10010.13740.08020.19140.02630.04950.15310.01110.222-24.96522.8164-56.4243
73.3881.132-0.30435.4187-1.01953.35220.1639-0.22910.56460.3685-0.1641-0.2-0.7257-0.10620.00820.4187-0.04170.02280.3571-0.02660.2963-23.380510.342-61.8287
81.8710.7067-0.02162.0321-0.72851.3475-0.05710.11970.0406-0.19250.08310.02070.0535-0.3488-0.03450.3521-0.0043-0.07180.3484-0.04240.2354-29.91350.601-62.4975
98.1837-3.6381-0.22966.77383.06284.9441-0.06170.4444-0.4222-0.3739-0.04910.00320.2911-0.37740.11550.4969-0.1386-0.07360.5235-0.03110.3268-27.9214-3.8508-72.4723
101.4305-0.4993-1.24963.9118-2.14742.873-0.1148-0.18260.23740.0784-0.0989-0.5625-0.20440.46310.24450.4123-0.1103-0.03170.4401-0.02890.3474-19.31222.8745-70.2243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 115 )A8 - 115
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 300 )A116 - 300
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 745 )A301 - 745
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 19 )B2 - 19
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 52 )B20 - 52
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 65 )B53 - 65
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 80 )B66 - 80
8X-RAY DIFFRACTION8chain 'B' and (resid 81 through 117 )B81 - 117
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 126 )B118 - 126
10X-RAY DIFFRACTION10chain 'B' and (resid 127 through 164 )B127 - 164

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