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- PDB-4qvt: Crystal structure of predicted N-acyltransferase (ypeA) in comple... -

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Basic information

Entry
Database: PDB / ID: 4qvt
TitleCrystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli
ComponentsAcetyltransferase YpeA
KeywordsTRANSFERASE / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / acetyltransferase
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
ACETYL COENZYME *A / Acetyltransferase YpeA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsFilippova, E.V. / Minasov, G. / Winsor, G. / Dubrovska, I. / Shuvalova, L. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli
Authors: Filippova, E.V. / Minasov, G. / Winsor, G. / Dubrovska, I. / Shuvalova, L. / Wolfe, A.J. / Anderson, W.F.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 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
C: Acetyltransferase YpeA
D: Acetyltransferase YpeA
E: Acetyltransferase YpeA
F: Acetyltransferase YpeA
G: Acetyltransferase YpeA
H: Acetyltransferase YpeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,83426
Polymers146,3978
Non-polymers7,43718
Water4,378243
1
A: Acetyltransferase YpeA
B: Acetyltransferase YpeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5077
Polymers36,5992
Non-polymers1,9075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-66 kcal/mol
Surface area13270 Å2
MethodPISA
2
C: Acetyltransferase YpeA
D: Acetyltransferase YpeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4116
Polymers36,5992
Non-polymers1,8114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-58 kcal/mol
Surface area13840 Å2
MethodPISA
3
E: Acetyltransferase YpeA
F: Acetyltransferase YpeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5077
Polymers36,5992
Non-polymers1,9075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-67 kcal/mol
Surface area13630 Å2
MethodPISA
4
G: Acetyltransferase YpeA
H: Acetyltransferase YpeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4116
Polymers36,5992
Non-polymers1,8114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-56 kcal/mol
Surface area13110 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39150 Å2
ΔGint-265 kcal/mol
Surface area45630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.334, 139.968, 75.358
Angle α, β, γ (deg.)90.00, 112.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetyltransferase YpeA


Mass: 18299.643 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b2434, JW2427, ypeA / Plasmid: pMCSG28 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Magic
References: UniProt: P76539, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate, 25% w/v PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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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: Jul 4, 2014 / Details: 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: 1.948→69.984 Å / Num. all: 92573 / Num. obs: 92573 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 33.8
Reflection shellResolution: 1.948→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.05 / Num. unique all: 4492 / % possible all: 95.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0069refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PDO
Resolution: 1.948→69.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.493 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23236 4600 5 %RANDOM
Rwork0.18813 ---
obs0.19033 87793 98.06 %-
all-87793 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å21.17 Å2
2--1.85 Å20 Å2
3----1.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.948→69.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 458 243 9841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199843
X-RAY DIFFRACTIONr_bond_other_d0.0010.029165
X-RAY DIFFRACTIONr_angle_refined_deg1.8712.01913348
X-RAY DIFFRACTIONr_angle_other_deg0.832321035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.87851136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.11323.857516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.218151679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9931596
X-RAY DIFFRACTIONr_chiral_restr0.1170.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0210992
X-RAY DIFFRACTIONr_gen_planes_other0.0180.022280
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_it3.3373.424555
X-RAY DIFFRACTIONr_mcbond_other3.2783.4154546
X-RAY DIFFRACTIONr_mcangle_it4.0275.0995682
X-RAY DIFFRACTIONr_mcangle_other4.0265.0985683
X-RAY DIFFRACTIONr_scbond_it4.8954.1515288
X-RAY DIFFRACTIONr_scbond_other4.8134.1315249
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5826.0777607
X-RAY DIFFRACTIONr_long_range_B_refined8.39916.62711180
X-RAY DIFFRACTIONr_long_range_B_other8.37616.59211126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.948→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 324 -
Rwork0.258 5987 -
obs--91.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2807-0.13921.04494.79430.49834.12580.0658-0.0881-0.03390.197-0.05060.59390.2929-0.4165-0.01520.03050.00460.01670.32810.00930.1613-49.8399-26.005588.9203
21.3431-0.602-1.87582.15830.30242.87380.1270.2617-0.0251-0.4285-0.13570.1993-0.0509-0.16210.00870.09950.0648-0.07010.44660.00910.1167-43.7188-23.51277.8251
31.1008-0.15440.41761.4306-0.19641.83820.01950.0207-0.02460.07160.01930.267-0.1883-0.18-0.03890.03730.04990.00710.28920.01430.0572-44.0755-14.841589.0506
45.8079-0.50511.72912.8519-0.80677.36340.09940.2345-0.1569-0.2072-0.4290.5628-0.0243-0.27810.32960.08690.1241-0.030.2163-0.09040.1573-45.9679-3.575778.7245
52.0799-0.4848-0.76364.5963-0.31441.04470.15990.30110.1512-0.4551-0.1631-0.1355-0.065-0.01790.00320.08750.037-0.00950.26640.01880.0389-33.8331-11.214878.0593
65.90350.5279-4.33644.64922.30417.09940.21970.3554-0.04270.0773-0.1427-0.71650.20730.0628-0.0770.06370.09340.01790.26730.03050.1869-10.2478-20.751888.152
73.0499-1.83920.48856.17921.04243.90140.0123-0.11880.34960.09670.2192-0.5501-0.30830.5487-0.23150.0449-0.0903-0.00940.26360.04350.1283-13.6484-7.173892.9647
81.1867-0.4073-0.56291.4009-0.40381.2260.12430.07260.1096-0.0605-0.1512-0.3065-0.1130.23220.02690.02960.00090.01230.33320.05010.0823-18.5889-15.041985.1084
95.18365.8216-2.433812.2268-4.73561.9048-0.0383-0.1294-0.0933-0.05770.0789-0.0673-0.0537-0.0376-0.04060.13590.02430.08380.11880.00340.0928-18.6562-6.374173
101.5661-0.7658-0.4931.8920.8013.16540.16290.14660.1302-0.2344-0.1691-0.109-0.2788-0.18210.00620.07860.02510.00510.18690.05680.0271-29.9981-6.87681.6879
112.55321.5474-0.45054.43820.14153.33030.0452-0.02450.06410.2387-0.1273-0.5402-0.24840.3940.08210.05670.0371-0.05010.35350.0050.1472-6.8639-36.645286.524
120.6310.166-0.38621.2897-0.16650.90890.0310.0425-0.045-0.019-0.0628-0.18340.06850.17810.03180.01780.0603-0.00790.3557-0.03270.0483-13.6301-44.514285.7803
133.20370.69990.28586.8205-0.19451.47190.06990.5061-0.3315-0.47620.0184-0.43630.1970.1987-0.08830.09170.0990.0020.285-0.09810.0704-13.9569-58.956579.4226
143.81834.473-1.17126.0405-0.55861.25-0.11120.1222-0.1315-0.35480.0851-0.1634-0.10690.0030.02610.20950.0847-0.02950.3995-0.03980.0601-25.2912-40.300672.2273
153.0232-0.50850.92784.9231-0.6653.79970.0571-0.1329-0.1190.19310.29450.6845-0.0058-0.5008-0.35160.0130.03230.0180.23330.020.1312-46.4062-47.692690.9742
161.2609-0.03530.00431.22-0.48260.84290.06490.2432-0.0963-0.16210.00480.21710.1105-0.1094-0.06970.02920.0213-0.03580.2959-0.06730.0555-38.4875-47.223483.5439
170.320.3101-0.02221.30470.10090.0301-0.06120.1668-0.2104-0.24620.02920.09870.02810.02820.0320.230.1265-0.08530.5569-0.14160.259-31.7954-56.026880.4233
180.07240.04460.5472.57721.69055.00920.1262-0.07650.0738-1.1611-0.7837-0.08940.1225-0.87120.65750.77320.22690.11820.47190.00140.2817-46.6782-49.5218106.184
193.13491.12331.44862.7791.22794.8079-0.0845-0.14250.09070.4189-0.27070.46230.0037-0.3190.35520.10050.00380.080.1728-0.03640.0921-44.3782-43.3724121.4761
200.71410.6052-0.17921.299-0.15040.9576-0.00040.0519-0.01990.0971-0.07760.19810.0956-0.03770.07810.06290.01010.03170.2557-0.01570.0677-38.1484-51.1667113.1019
212.93361.2075-0.08091.5861-1.40191.73320.0483-0.2351-0.24780.0927-0.1554-0.1696-0.04680.08620.10710.1970.03850.05080.34140.06540.0706-29.574-57.2587121.9763
2210.36823.9526-0.69021.92420.62341.9298-0.183-0.12420.3161-0.12250.02690.2019-0.1010.15680.15610.15420.05210.04150.1128-0.00860.073-39.6699-39.0071132.5983
2311.30341.5966-0.51155.12472.32551.30240.1341-0.21320.65890.07730.0999-0.32250.04030.1581-0.2340.1145-0.0367-0.02940.1843-0.02050.0845-8.1875-35.3622113.9854
241.41190.9235-1.11622.3899-0.33274.7307-0.1114-0.0135-0.37090.03730.1694-0.30790.00890.6521-0.0580.09520.08510.02070.4104-0.00440.1559-8.1475-49.9756108.6081
252.3187-0.2741-0.21170.75830.50160.6473-0.1413-0.2085-0.07960.21350.1002-0.0802-0.03040.28440.04110.18410.0003-0.07590.43750.04310.0422-14.458-42.4062117.6451
2612.0649-7.5116-4.70355.95133.7833.3386-0.1413-0.4483-0.21890.47460.1538-0.24830.06820.408-0.01250.34240.0539-0.14990.32310.11770.1855-12.2395-52.504129.5667
274.25560.7189-1.36192.0132-0.91460.8687-0.2332-0.2979-0.94270.1894-0.2326-0.47540.1491-0.12140.46580.2716-0.16730.06830.53490.03330.2763-21.5833-55.5326117.9981
284.0107-1.08162.45963.6511-3.07968.33420.32390.1457-0.482-0.1251-0.02910.26950.3559-0.2758-0.29480.0504-0.0067-0.03480.0943-0.01280.0689-49.5212-27.6503110.6843
291.5371.8210.02477.543-0.51244.5560.0137-0.0019-0.05370.37330.16190.6246-0.3507-0.5378-0.17560.05120.07340.05050.19120.02340.0931-51.6434-13.047111.6874
300.7862-0.1056-0.31491.5603-0.19251.28910.0014-0.0321-0.07150.29580.03570.2565-0.1029-0.1581-0.03720.14150.01070.03850.2857-0.00460.049-43.302-20.3598117.7821
316.5395-5.42590.65945.57690.81231.82140.16050.0761-0.03860.1688-0.11350.03540.3208-0.1034-0.04690.29350.00120.14740.1935-0.0120.1083-44.2142-16.1024131.7961
322.76350.48440.20162.77980.81420.2566-0.1210.00230.76980.08310.03970.1458-0.05370.06340.08130.406-0.1315-0.11610.36420.01680.2313-34.4715-5.8352116.7281
335.62164.829-2.841413.158-1.5141.57010.442-0.0294-0.20950.4437-0.569-0.5825-0.2390.08930.1270.054-0.0764-0.06290.50090.21290.135-11.5247-15.2613108.6506
343.97720.1449-2.21674.02393.66868.28660.05880.0814-0.18120.33220.1373-0.81260.04850.5832-0.19620.0460.0071-0.09420.2890.06190.2316-9.4437-25.0793114.2614
351.01120.14060.17642.2368-0.31571.82910.0148-0.0930.07020.3962-0.1765-0.361-0.27760.36460.16170.195-0.0881-0.11020.38680.0250.0847-18.3915-14.0654117.3414
3612.678-6.28214.54496.76652.25667.2098-0.1927-0.01540.64780.1569-0.0508-0.29280.0024-0.02220.24350.2557-0.1415-0.06730.1957-0.0230.0722-20.4502-1.284122.9499
371.70630.0565-0.55755.35510.10771.87460.0376-0.23770.18060.6659-0.19570.136-0.25080.0680.15810.2465-0.0434-0.07080.249-0.03990.0783-30.3894-11.0905124.7335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION2A17 - 38
3X-RAY DIFFRACTION3A39 - 109
4X-RAY DIFFRACTION4A110 - 119
5X-RAY DIFFRACTION5A120 - 139
6X-RAY DIFFRACTION6B1 - 6
7X-RAY DIFFRACTION7B7 - 27
8X-RAY DIFFRACTION8B28 - 111
9X-RAY DIFFRACTION9B112 - 118
10X-RAY DIFFRACTION10B119 - 139
11X-RAY DIFFRACTION11C1 - 20
12X-RAY DIFFRACTION12C21 - 108
13X-RAY DIFFRACTION13C109 - 127
14X-RAY DIFFRACTION14C128 - 141
15X-RAY DIFFRACTION15D1 - 20
16X-RAY DIFFRACTION16D21 - 112
17X-RAY DIFFRACTION17D113 - 146
18X-RAY DIFFRACTION18E1 - 5
19X-RAY DIFFRACTION19E6 - 33
20X-RAY DIFFRACTION20E34 - 111
21X-RAY DIFFRACTION21E112 - 136
22X-RAY DIFFRACTION22E137 - 145
23X-RAY DIFFRACTION23F1 - 6
24X-RAY DIFFRACTION24F7 - 33
25X-RAY DIFFRACTION25F34 - 109
26X-RAY DIFFRACTION26F110 - 119
27X-RAY DIFFRACTION27F120 - 141
28X-RAY DIFFRACTION28G1 - 9
29X-RAY DIFFRACTION29G10 - 26
30X-RAY DIFFRACTION30G27 - 111
31X-RAY DIFFRACTION31G112 - 123
32X-RAY DIFFRACTION32G124 - 141
33X-RAY DIFFRACTION33H1 - 6
34X-RAY DIFFRACTION34H7 - 13
35X-RAY DIFFRACTION35H14 - 112
36X-RAY DIFFRACTION36H113 - 118
37X-RAY DIFFRACTION37H119 - 138

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