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- PDB-8zt4: Complex structure of N-acetyltransferase SbzI and carrier protein... -

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Basic information

Entry
Database: PDB / ID: 8zt4
TitleComplex structure of N-acetyltransferase SbzI and carrier protein SbzG in the biosynthesis of altemicidin
ComponentsCarrier protein,GNAT family transferase
KeywordsTRANSFERASE / A general control non-repressible 5 (GCN5)-related N-acetyltransferase / altemicidin / biosynthesis
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
BICARBONATE ION / THIOCYANATE ION / GNAT family transferase / Carrier protein
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhu, Y. / Mori, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structure-function analysis of carrier protein-dependent 2-sulfamoylacetyl transferase in the biosynthesis of altemicidin.
Authors: Zhu, Y. / Mori, T. / Karasawa, M. / Shirai, K. / Cheng, W. / Terada, T. / Awakawa, T. / Abe, I.
History
DepositionJun 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carrier protein,GNAT family transferase
B: Carrier protein,GNAT family transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,17211
Polymers63,6832
Non-polymers4899
Water84747
1
A: Carrier protein,GNAT family transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1737
Polymers31,8421
Non-polymers3326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carrier protein,GNAT family transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9994
Polymers31,8421
Non-polymers1573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.150, 95.680, 130.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Carrier protein,GNAT family transferase


Mass: 31841.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: sbzG, sbzI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3T0ZHH1, UniProt: A0A3T0ZHG5
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: CHO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.83 Å3/Da / Density % sol: 67.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES, pH 6.5, 0.2 M KSCN, 15% PEG 8000, 3% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→47.84 Å / Num. obs: 30470 / % possible obs: 99.9 % / Redundancy: 18 % / Biso Wilson estimate: 61.43 Å2 / CC star: 0.997 / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.3
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 18.9 % / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 3652 / CC1/2: 0.947 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.6→47.84 Å / SU ML: 0.327 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.2239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 2000 6.58 %
Rwork0.1959 28416 -
obs0.1984 30416 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.59 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 69 47 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463920
X-RAY DIFFRACTIONf_angle_d0.70685321
X-RAY DIFFRACTIONf_chiral_restr0.0408599
X-RAY DIFFRACTIONf_plane_restr0.0071706
X-RAY DIFFRACTIONf_dihedral_angle_d13.42931412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.37551420.28912004X-RAY DIFFRACTION99.63
2.67-2.740.28831380.22881977X-RAY DIFFRACTION99.86
2.74-2.820.24951400.22471988X-RAY DIFFRACTION99.77
2.82-2.910.28631420.24882009X-RAY DIFFRACTION99.91
2.91-3.010.41311400.29282002X-RAY DIFFRACTION99.86
3.01-3.130.26561420.25552014X-RAY DIFFRACTION99.95
3.13-3.280.29461410.22752000X-RAY DIFFRACTION99.95
3.28-3.450.26781430.222036X-RAY DIFFRACTION100
3.45-3.660.30711420.22732025X-RAY DIFFRACTION100
3.66-3.950.22051420.18982020X-RAY DIFFRACTION99.91
3.95-4.340.19381440.16172040X-RAY DIFFRACTION99.86
4.34-4.970.18761450.15632044X-RAY DIFFRACTION99.64
4.97-6.260.21361450.1872073X-RAY DIFFRACTION99.69
6.26-47.840.19971540.17362184X-RAY DIFFRACTION99.87
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)
19.23961.17323.62695.77581.21939.3210.0464-0.6934-0.1677-0.00210.1429-0.050.0895-0.061-0.18640.46730.10520.05020.49350.00720.4402-4.00321.82964.9117
24.4214-0.64281.12472.7885-0.40753.2203-0.13330.3135-0.0193-0.10080.0839-0.15360.07850.23150.09360.523-0.06280.04660.3881-0.03140.3674-8.729120.1363-19.8457
34.82810.5878-0.72765.6440.15984.3023-0.06610.25330.75340.03070.23470.1672-0.4564-0.3159-0.16990.4393-0.04630.00990.43230.03670.4672-14.546131.6104-14.9135
46.53562.59064.65956.39520.15464.3694-0.53670.16190.9170.6652-0.1399-1.64520.37041.85810.64040.81270.0292-0.08291.5316-0.41161.61234.467550.853725.7036
58.7365-0.771.15797.8349-4.30068.4806-0.0526-0.3407-0.67750.92680.5656-1.9243-0.11550.9797-0.49510.75230.1849-0.24191.3347-0.57141.4934-4.76348.307331.8742
65.06571.45452.31044.45732.00683.4583-0.13270.13020.2009-0.4690.1564-0.1196-0.50040.33130.02340.50650.02450.00740.4562-0.07840.3753-28.173751.443921.1312
74.4322-6.24473.74439.391-5.6053.47490.2694-0.1484-1.187-0.5257-0.1429-0.30161.14030.4593-0.17490.8120.0635-0.11230.6549-0.06750.8679-26.320729.061819.5134
84.0972.75590.77717.53021.01543.4029-0.27210.2429-0.2111-0.63620.7424-1.1916-0.0390.8481-0.42310.57080.02950.05280.7405-0.19270.6169-18.455143.965420.5812
90.11360.4884-0.34163.43650.5132.0925-0.38510.34790.1168-0.8165-0.1846-0.77530.93730.80510.46180.7759-0.00010.22810.9854-0.28780.8452-18.434934.122511.2027
1022.00011.999921.99992.00026.556220.6267.0675-10.9348-9.497512.54566.8411-3.66423.02681.20450.1696-0.3180.9585-0.20461.9939-16.531531.585234.3126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 159 )
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 268 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 37 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 168 )
7X-RAY DIFFRACTION7chain 'B' and (resid 169 through 185 )
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 242 )
9X-RAY DIFFRACTION9chain 'B' and (resid 243 through 267 )
10X-RAY DIFFRACTION10chain 'B' and (resid 268 through 268 )

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