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- PDB-4rs2: 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4rs2
Title1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from Escherichia coli in Complex with CoA
ComponentsPredicted acyltransferase with acyl-CoA N-acyltransferase domain
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / GNAT Family N-acetyltransferase / N-acetyltransferase / CoA
Function / homologyGcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / COENZYME A / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsMinasov, G. / Wawrzak, Z. / Kuhn, M. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from Escherichia coli in Complex with CoA.
Authors: Minasov, G. / Wawrzak, Z. / Kuhn, M. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Data collection
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted acyltransferase with acyl-CoA N-acyltransferase domain
B: Predicted acyltransferase with acyl-CoA N-acyltransferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3284
Polymers41,7932
Non-polymers1,5352
Water8,251458
1
A: Predicted acyltransferase with acyl-CoA N-acyltransferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6642
Polymers20,8961
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Predicted acyltransferase with acyl-CoA N-acyltransferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6642
Polymers20,8961
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.863, 44.658, 57.023
Angle α, β, γ (deg.)80.40, 80.25, 90.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Predicted acyltransferase with acyl-CoA N-acyltransferase domain / GNAT Family N-acetyltransferase (YhbS)


Mass: 20896.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: strain K-12, substrain MG1655 / Gene: ECMDS42_2623, yhbS / Plasmid: pCA24N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Magic / References: UniProt: H0QE96
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 7.8mg/ml, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PACT (D2), 0.1M MMT buffer (pH 5.0), 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2014 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 44460 / Num. obs: 44460 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 16.2
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2148 / Rsym value: 0.544 / % possible all: 95

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→27.69 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.037 / SU ML: 0.06
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20328 2236 5.1 %RANDOM
Rwork0.16425 ---
obs0.16621 41929 96.63 %-
all-41929 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.316 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0.3 Å20.03 Å2
2--0.38 Å20.26 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 96 458 3398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193326
X-RAY DIFFRACTIONr_bond_other_d0.0010.022978
X-RAY DIFFRACTIONr_angle_refined_deg1.652.0184580
X-RAY DIFFRACTIONr_angle_other_deg0.77136846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9475405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77723.626171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58815481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4591528
X-RAY DIFFRACTIONr_chiral_restr0.0960.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023884
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02822
X-RAY DIFFRACTIONr_mcbond_it1.1281.0081560
X-RAY DIFFRACTIONr_mcbond_other1.1251.0081559
X-RAY DIFFRACTIONr_mcangle_it1.8721.5081985
X-RAY DIFFRACTIONr_mcangle_other1.8721.5091986
X-RAY DIFFRACTIONr_scbond_it1.5921.2181766
X-RAY DIFFRACTIONr_scbond_other1.5911.2181767
X-RAY DIFFRACTIONr_scangle_other2.4871.7652596
X-RAY DIFFRACTIONr_long_range_B_refined6.18110.3394144
X-RAY DIFFRACTIONr_long_range_B_other5.9319.3423892
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 169 -
Rwork0.22 3041 -
obs-3041 94.97 %
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)
12.46230.06510.60141.11190.51040.9218-0.029-0.15210.24310.16610.0754-0.0633-0.13760.0284-0.04640.1108-0.0127-0.00150.0887-0.02720.080521.712428.969123.9737
21.25140.3679-0.00511.4551-0.13280.74910.0639-0.15050.08260.089-0.05340.0054-0.0061-0.0122-0.01060.0377-0.01320.00390.0549-0.00050.008312.637817.891920.7984
30.96930.32950.05631.30680.16750.49320.01060.0414-0.0235-0.0277-0.0288-0.07580.02080.03330.01820.02150.00770.00880.02920.01170.014620.664111.843812.6985
42.4292-0.41961.05483.82370.03862.6913-0.03270.06130.0257-0.08460.0415-0.02410.0068-0.0154-0.00890.0046-0.00630.00610.0613-0.00250.02515.965215.328511.3331
51.7999-0.24350.43351.0956-0.330.69270.02220.11190.0835-0.0465-0.00220.0454-0.00620.0262-0.020.03960.00340.00980.05870.01010.011111.004311.6538.2433
61.7136-2.3520.71978.7112-2.52121.18080.12160.13980.1249-0.1256-0.1461-0.05670.05560.00660.02450.03590.00430.00330.05610.00650.013911.2054.970140.3653
71.088-0.06710.06181.722-0.13760.46590.034-0.0368-0.01870.0469-0.06340.11980.0205-0.02350.02940.0178-0.00320.01020.0263-0.00990.01577.0199-1.412947.9501
82.2918-0.14821.49083.10781.29334.1608-0.011-0.04690.04840.11830.072-0.08660.032-0.0008-0.0610.0113-0.00040.00520.04630.01040.021721.33813.285849.805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 23
2X-RAY DIFFRACTION2A24 - 70
3X-RAY DIFFRACTION3A71 - 158
4X-RAY DIFFRACTION4A159 - 172
5X-RAY DIFFRACTION5B-10 - 47
6X-RAY DIFFRACTION6B48 - 67
7X-RAY DIFFRACTION7B68 - 159
8X-RAY DIFFRACTION8B160 - 172

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