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- PDB-4qus: 1.28 Angstrom resolution crystal structure of predicted acyltrans... -

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Basic information

Entry
Database: PDB / ID: 4qus
Title1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655
ComponentsAcetyltransferase YpeA
KeywordsTRANSFERASE / predicted acyltransferase / acyl-CoA N-acyltransferase domain / GNAT acetyltransferase / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase, YpeA / : / 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
PHOSPHATE ION / Acetyltransferase YpeA
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Minasov, G. / Flores, K.J. / Dubrovska, I. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655
Authors: Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Flores, K.J. / Dubrovska, I. / Shuvalova, L. / Anderson, W.F.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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 / 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_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: Acetyltransferase YpeA
B: Acetyltransferase YpeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8877
Polymers34,5112
Non-polymers3765
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-19 kcal/mol
Surface area14560 Å2
MethodPISA
2
A: Acetyltransferase YpeA
B: Acetyltransferase YpeA
hetero molecules

A: Acetyltransferase YpeA
B: Acetyltransferase YpeA
hetero molecules

A: Acetyltransferase YpeA
B: Acetyltransferase YpeA
hetero molecules

A: Acetyltransferase YpeA
B: Acetyltransferase YpeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,54928
Polymers138,0448
Non-polymers1,50520
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area32670 Å2
ΔGint-88 kcal/mol
Surface area48770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.817, 90.817, 84.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Acetyltransferase YpeA / predicted acyltransferase with acyl-CoA N-acyltransferase domain


Mass: 17255.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: b2434, JW2427, ypeA / Plasmid: pMCSG28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Magic
References: UniProt: P76539, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 7 mg/mL protein (no tag) in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: the PACT Suite A6 (#6): 0.1 M SPG buffer, pH 9.0, 25% w/v PEG1500, cryo-protection: ...Details: 7 mg/mL protein (no tag) in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: the PACT Suite A6 (#6): 0.1 M SPG buffer, pH 9.0, 25% w/v PEG1500, cryo-protection: well solution soak, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2014 / Details: Bimorph K-B pair mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.28→30 Å / Num. all: 87246 / Num. obs: 87246 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.25
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PDO

2pdo


Resolution: 1.28→28.72 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.002 / SU ML: 0.02 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13859 4387 5 %RANDOM
Rwork0.10935 ---
obs0.11083 82845 99.74 %-
all-82845 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.899 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.28→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 22 537 2902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192609
X-RAY DIFFRACTIONr_bond_other_d0.0010.022457
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.973540
X-RAY DIFFRACTIONr_angle_other_deg0.87735652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1315326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48524.11146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.09315469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2491526
X-RAY DIFFRACTIONr_chiral_restr0.1010.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023075
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02623
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.14335066
X-RAY DIFFRACTIONr_sphericity_free53.156570
X-RAY DIFFRACTIONr_sphericity_bonded11.86455488
LS refinement shellResolution: 1.28→1.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 314 -
Rwork0.19 6014 -
obs--98.51 %
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)
15.5907-3.2571-4.5263.06261.79267.6081-0.00870.22180.2427-0.0710.0646-0.1705-0.16590.0743-0.05590.1094-0.05430.01860.13390.01840.1179101.51778.24-45.768
20.7257-0.005-0.11450.4140.04870.3494-0.01210.1313-0.0693-0.0443-0.006-0.01440.0056-0.04090.01810.0059-0.00230.00680.025-0.01370.030896.977471.201-39.2885
33.20190.2582-1.8270.88460.66465.3646-0.15580.2633-0.2253-0.07590.0852-0.05760.4201-0.07340.07060.0938-0.00210.01420.0314-0.01710.1106.389259.5424-35.9038
41.1777-0.4909-0.1910.6255-0.27470.7508-0.0314-0.0509-0.2538-0.01360.03340.06480.1173-0.0461-0.0020.0766-0.00390.0020.0348-0.00410.117894.284360.3584-25.7291
57.10741.8871-0.00863.1955-0.88472.54760.0666-0.50620.02390.1598-0.07460.2141-0.1239-0.25930.0080.04880.03390.00290.1328-0.00140.047191.514276.8732-5.2779
60.9735-0.01550.36990.36850.05440.4924-0.0188-0.194-0.10660.08470.0214-0.0350.0272-0.0668-0.00260.02130.0093-0.0020.04370.02670.033497.619470.9295-11.2613
710.2764-1.1884-2.83584.6280.20463.9905-0.241-1.0424-0.81710.34670.00320.02280.52830.25370.23790.1550.02910.02760.12490.11720.152795.757154.0575-14.3895
80.38470.1980.360.59770.05770.8957-0.0422-0.0105-0.08770.0061-0.0014-0.0621-0.00970.07890.04360.01810.01620.00210.02350.00950.0789112.503570.4796-18.8906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 103
3X-RAY DIFFRACTION3A104 - 122
4X-RAY DIFFRACTION4A123 - 140
5X-RAY DIFFRACTION5B1 - 7
6X-RAY DIFFRACTION6B8 - 108
7X-RAY DIFFRACTION7B109 - 125
8X-RAY DIFFRACTION8B126 - 149

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