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- PDB-2pr1: Crystal structure of the Bacillus subtilis N-acetyltransferase Yl... -

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Basic information

Entry
Database: PDB / ID: 2pr1
TitleCrystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A
ComponentsUncharacterized N-acetyltransferase ylbP
KeywordsTRANSFERASE / N-acetyltransferase / YibP protein / Coenzyme A / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Putative N-acetyltransferase YlbP / 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
sucrose / : / COENZYME A / Uncharacterized N-acetyltransferase YlbP
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Vorontsov, I.I. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Vorontsov, I.I. / Collart, F.R. / Joachimiak, A. / Anderson, W.F.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT A DIMER WITH THE ASSEMBLY SHOWN IN REMARK 350 IS PROBABLY THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,20410
Polymers38,6742
Non-polymers2,5308
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-59 kcal/mol
Surface area16960 Å2
MethodPISA
2
A: Uncharacterized N-acetyltransferase ylbP
B: Uncharacterized N-acetyltransferase ylbP
hetero molecules

A: Uncharacterized N-acetyltransferase ylbP
B: Uncharacterized N-acetyltransferase ylbP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,40720
Polymers77,3484
Non-polymers5,05916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area12770 Å2
ΔGint-133 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.572, 148.572, 102.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a dimer generated from the peptide chains A and B of the asymmetric unit.

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Uncharacterized N-acetyltransferase ylbP


Mass: 19337.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ylbP, BSU15100 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O34468, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 29 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01M Cobalt chloride, 0.25M Sodium chloride, 0.1M MES, 1.8M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2007 / Details: K-B pair biomorph mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 11325 / Num. obs: 11325 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.3
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1104 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.88 / SU B: 32.411 / SU ML: 0.292 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.437
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25462 1101 9.7 %RANDOM
Rwork0.21548 ---
obs0.21934 10209 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 76.773 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20.82 Å20 Å2
2--1.63 Å20 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 154 23 2718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222761
X-RAY DIFFRACTIONr_angle_refined_deg1.562.0293735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7275299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89624.203138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08315493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4881517
X-RAY DIFFRACTIONr_chiral_restr0.1080.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022029
X-RAY DIFFRACTIONr_nbd_refined0.2170.21184
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.23
X-RAY DIFFRACTIONr_mcbond_it0.7971.51545
X-RAY DIFFRACTIONr_mcangle_it1.30522422
X-RAY DIFFRACTIONr_scbond_it2.08331395
X-RAY DIFFRACTIONr_scangle_it3.5184.51313
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 81 -
Rwork0.249 731 -
obs-731 99.51 %
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)
117.41482.79252.56826.37731.56911.7615-0.2007-0.052-1.1259-0.26610.09060.00290.84090.13170.1101-0.21430.04430.3359-0.16490.23880.1299122.736722.88197.6943
24.5068-0.82460.79772.55270.76355.5636-0.33390.2861-0.2024-0.5005-0.1421-0.0693-0.03170.44870.476-0.2967-0.00150.3219-0.17860.2476-0.0661124.16932.46718.3021
34.6196-1.19580.77766.35462.74214.4399-0.2756-0.425-0.4960.4825-0.0453-0.3850.45080.59380.3209-0.30850.15490.31060.02270.3995-0.0297128.761528.717319.0757
412.916-12.0737-3.785213.28524.60251.6758-0.3649-1.0697-1.17571.25130.10880.83260.2306-0.05420.2561-0.1783-0.0481-0.01080.09360.418-0.0798124.005736.995527.4286
542.8952-6.3115-5.964411.96423.31057.3178-0.4587-0.1648-1.58510.43530.0641-1.71830.1751.45480.3946-0.0978-0.01680.11710.21840.26870.0532131.584737.115426.8693
614.3591-8.31666.751312.4867-4.959514.9517-0.559-1.5809-0.67850.86970.6950.3201-0.0823-0.8748-0.136-0.35270.05410.0748-0.07810.2534-0.2506103.714744.622736.8293
78.1328-1.72333.07853.05341.76217.0931-0.2377-0.73750.37990.3879-0.2219-0.4874-0.95420.79850.4597-0.1640.0445-0.0117-0.27470.1972-0.2365109.632149.051930.9561
85.5002-0.124-0.27175.9937-2.42078.8187-0.14170.5917-0.2138-0.08750.0731-0.1359-0.1941-0.32430.0686-0.34690.14370.0784-0.3080.0408-0.4313101.008345.959522.6069
918.7457-0.0915-4.6860.23710.44231.9148-0.39530.9109-1.8736-0.2172-0.2509-0.48120.3766-0.28290.6462-0.11660.05190.0486-0.17610.1598-0.2028107.745341.248313.2162
1042.8856-25.3514-13.510633.52437.63794.26290.92551.75580.9792-2.4989-1.5389-0.0389-0.58710.38250.6134-0.1211-0.1127-0.0281-0.02840.1603-0.5901106.009147.294411.1407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 224 - 25
2X-RAY DIFFRACTION2AA23 - 7526 - 78
3X-RAY DIFFRACTION3AA76 - 10879 - 111
4X-RAY DIFFRACTION4AA109 - 139112 - 142
5X-RAY DIFFRACTION5AA140 - 152143 - 155
6X-RAY DIFFRACTION6BB2 - 225 - 25
7X-RAY DIFFRACTION7BB23 - 7526 - 78
8X-RAY DIFFRACTION8BB76 - 10879 - 111
9X-RAY DIFFRACTION9BB109 - 139112 - 142
10X-RAY DIFFRACTION10BB140 - 150143 - 153

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