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- PDB-7kyj: Structure of a GNAT superfamily PA3944 acetyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 7kyj
TitleStructure of a GNAT superfamily PA3944 acetyltransferase in complex with zinc
ComponentsAcetyltransferase PA3944
KeywordsTRANSFERASE / PA3944 / acetyltransferase / GNAT Superfamily / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Acyl-CoA N-acyltransferase / ACETATE ION / COENZYME A / Acetyltransferase PA3944
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCzub, M.P. / Porebski, P.J. / Cymborowski, M. / Shabalin, I.G. / Reidl, C.T. / Becker, D.P. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structure of a GNAT superfamily PA3944 acetyltransferase in complex with zinc
Authors: Czub, M.P. / Porebski, P.J. / Cymborowski, M. / Shabalin, I.G. / Minor, W.
History
DepositionDec 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase PA3944
B: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,00611
Polymers44,1602
Non-polymers1,8469
Water3,135174
1
A: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9726
Polymers22,0801
Non-polymers8925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0345
Polymers22,0801
Non-polymers9544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.423, 43.801, 60.793
Angle α, β, γ (deg.)98.050, 109.510, 90.100
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 8 - 191 / Label seq-ID: 10 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetyltransferase PA3944 / GCN5-related N-acetyltransferase / GNAT


Mass: 22080.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3944 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HX72, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 6 types, 183 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 uL of 8 mg/mL protein incubated with 2.5 mM CoA was mixed with 0.2 uL of the well condition (MCSG suite I condition 11 - 100 mM Tris-HCl pH 7.0, 200 mM calcium acetate, 20% w/v PEG 3000) ...Details: 0.3 uL of 8 mg/mL protein incubated with 2.5 mM CoA was mixed with 0.2 uL of the well condition (MCSG suite I condition 11 - 100 mM Tris-HCl pH 7.0, 200 mM calcium acetate, 20% w/v PEG 3000) and equilibrated against well solution in 96 Well 3 drop Crystallization Plate (Swissci). The obtained crystals were soaked with 10 mM (R)-3-(2-chloroacetamido)-4-(((S)-1-methoxy-1-oxo-3-phenylpropan-2-yl)amino)-4-oxobutanoic acid.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.893
11H, -K, -H-L20.107
ReflectionResolution: 2→50 Å / Num. obs: 22739 / % possible obs: 97.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.107 / Rrim(I) all: 0.151 / Χ2: 0.61 / Net I/σ(I): 10.6 / Num. measured all: 43598
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.031.80.45511130.3790.4550.6440.74695.8
2.03-2.071.80.4511290.3450.450.6370.82295.8
2.07-2.111.80.36811330.4380.3680.520.7796.5
2.11-2.151.90.33311430.5710.3330.4720.73596.9
2.15-2.21.90.3310900.5930.330.4660.72597.1
2.2-2.251.90.34511530.5150.3450.4880.78896.2
2.25-2.311.90.39111210.4070.3910.5530.78897.1
2.31-2.371.90.30611550.5930.3060.4330.797.6
2.37-2.4420.27311190.6480.2730.3860.67297.4
2.44-2.5220.25911330.6240.2590.3670.56897.8
2.52-2.6120.24111440.6340.2410.340.61197.7
2.61-2.7120.20111480.6640.2010.2840.53997.4
2.71-2.8420.17311580.7440.1730.2440.51598.3
2.84-2.9920.12711500.8610.1270.1790.46398
2.99-3.171.90.10911190.8880.1090.1540.45498.5
3.17-3.4220.07811490.9370.0780.1110.46698.5
3.42-3.761.90.07311520.9250.0730.1040.56297.5
3.76-4.311.90.06311530.9430.0630.090.54698.2
4.31-5.431.90.05711430.960.0570.080.50798.8
5.43-501.90.04611340.9680.0460.0650.3297

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EDD

6edd


Resolution: 2→32.17 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 10.129 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 1070 5.2 %RANDOM
Rwork0.1998 ---
obs0.2021 19513 87.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.09 Å2 / Biso mean: 31.369 Å2 / Biso min: 12.81 Å2
Baniso -1Baniso -2Baniso -3
1--10.94 Å2-3.53 Å2-4.78 Å2
2--0.03 Å22.15 Å2
3---10.91 Å2
Refinement stepCycle: final / Resolution: 2→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 112 174 3311
Biso mean--29.78 33.33 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133252
X-RAY DIFFRACTIONr_bond_other_d0.0180.0172938
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.6584436
X-RAY DIFFRACTIONr_angle_other_deg1.491.5756711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.55918.756209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7615459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9181543
X-RAY DIFFRACTIONr_chiral_restr0.060.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023690
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02842
Refine LS restraints NCS

Ens-ID: 1 / Number: 6123 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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)
113.1197-1.745-7.41911.54151.724114.344-0.2602-0.5353-0.44330.1546-0.03070.42560.4563-1.02190.29090.22680.01350.04450.22020.0080.17222.815-0.9248.35
25.21081.38031.274.2138-0.677717.04990.0217-0.078-0.1677-0.1476-0.02190.04380.81420.09050.00020.11330.02580.04680.0705-0.02490.11298.07-2.48414.868
37.42815.16430.41774.11450.91920.79420.12880.0189-0.480.14-0.0279-0.37730.0287-0.0181-0.10090.2230.02540.04070.19960.04270.170720.2641.36619.74
42.72330.6626-4.64864.2004-1.92818.10640.0858-0.2271-0.0603-0.0617-0.2259-0.1073-0.07710.39930.14010.2311-0.01950.03640.30530.00440.155223.30911.47921.324
525.3195-9.67336.80344.2333-4.31517.61470.3272-0.0502-0.0669-0.0367-0.1310.04850.08240.3821-0.19610.322-0.0585-0.01480.2117-0.00730.197114.3893.8326.889
616.1144-3.89390.243511.008-4.439110.787-0.2652-0.44840.17190.48820.1013-0.0914-0.06720.02840.16390.10340.00910.05250.0882-0.03840.06471.7986.82622.094
74.4391-5.4974-4.147110.05564.53516.1753-0.03180.27350.10760.0733-0.0206-0.21830.3035-0.06540.05240.1349-0.00910.06430.1076-0.00220.04488.7830.06810.942
80.8653-1.0498-0.03245.89570.94420.5911-0.0667-0.12770.08710.33230.10860.1423-0.04180.0213-0.04180.1628-0.00510.0720.1265-0.03390.05847.94113.71516.679
99.6093-6.9690.35615.7705-0.20021.2857-0.1465-0.2654-0.02720.29390.0137-0.03220.06470.09030.13280.1614-0.02320.06290.1088-0.00150.095713.36210.11212.432
105.9302-2.3546-0.52061.28090.07971.11510.10690.1298-0.1974-0.1563-0.10020.2096-0.041-0.1229-0.00660.16090.02760.04180.0901-0.02260.12726.9698.2375.217
113.4741-1.5184-0.0345.15541.47231.23110.13820.27660.26820.02660.0485-0.357-0.03960.1548-0.18680.17590.02340.07920.08790.00130.073716.48818.52910.511
122.1048-0.36630.60891.98560.58074.16340.0095-0.08260.04170.03770.02580.0827-0.27220.1581-0.03530.14530.01730.09670.0551-0.01380.098814.4522.79210.912
1322.909-2.672913.05366.49-6.749523.64850.2436-0.5307-0.66990.4553-0.46520.39290.05090.9340.22170.19120.01380.01070.2372-0.01090.170922.69924.54823.662
147.5254-0.32514.76361.210.65697.4578-0.0908-0.53660.2841-0.0827-0.04960.0662-0.2025-0.53290.14030.19340.03120.07870.0888-0.02030.09910.12923.0569.1
1518.5951-12.46815.5910.2679-3.037341.89690.79061.42310.1398-0.649-0.9837-0.06850.21771.09460.1930.564-0.11810.12180.36190.01370.28453.37817.292-2.038
1611.1624-0.66981.90080.0574-0.1310.3564-0.404-2.4656-0.0255-0.01910.2323-0.0607-0.0698-0.46680.17180.9292-0.0517-0.06851.0798-0.01861.055414.36713.44323.628
1715.8013-6.9587-29.46429.691619.668566.6292-0.35830.2348-0.3501-0.7855-0.2252-0.1781.12750.27920.58340.64490.14080.02210.5141-0.05360.372816.74810.76441.332
182.4274-2.49370.55533.3638-0.94473.44440.08210.2928-0.003-0.1617-0.2975-0.14280.51080.12430.21550.34450.00510.12150.1724-0.03230.14055.73311.18542.61
1921.0465-14.09160.282610.14761.60914.5512-0.1721-0.1404-0.67840.17150.13410.47180.10240.08560.0380.2006-0.00210.06180.1977-0.03770.1422-7.73916.43136.897
201.45510.2265-1.73018.01493.3334.31720.00030.05960.0192-0.3114-0.01670.2803-0.1870.32240.01640.15360.04080.04170.297-0.02250.1065-7.52423.00435.72
2110.89531.60614.66372.01451.88186.4509-0.06360.3115-0.0304-0.04980.08260.0878-0.12210.0712-0.01890.14390.01750.07540.0638-0.02140.07049.63319.69333.465
220.98740.67820.48866.94540.51013.66680.019-0.11610.01360.2641-0.04930.09430.1846-0.07570.03040.11850.02850.07820.0802-0.0030.06584.01612.78845.506
231.66010.8225-0.53022.6162-0.04861.2552-0.07190.21990.128-0.23190.1538-0.0547-0.082-0.1125-0.08190.18870.05740.07240.1182-0.01230.09574.14125.97943.982
2419.09745.806-1.5818.1599-1.10731.35430.3237-0.2378-0.04210.736-0.1333-0.0337-0.09770.1017-0.19050.14910.0050.04010.09-0.02660.061211.03121.39451.832
2511.5575-2.44322.63582.0323-0.29722.12-0.07180.02010.05040.04960.0465-0.1108-0.03910.14580.02530.16160.02120.09120.0716-0.02720.092610.00729.83947.252
261.63541.49730.90326.31730.69721.64660.0128-0.02130.1463-0.01270.05080.2044-0.1524-0.0885-0.06360.12360.03820.0760.076-0.02320.09780.10933.75951.623
276.41471.70843.77076.928110.235838.85090.08280.7144-0.5562-0.60630.30910.13090.41750.3332-0.39190.243-0.01840.02480.1294-0.01270.17061.15238.60836.393
286.14332.05746.624724.9955-9.014612.3427-0.4168-0.1230.1049-1.04620.36890.2656-0.0627-0.30790.0480.3942-0.0703-0.06440.279-0.03730.3773-6.31938.45232.391
298.5385-1.38124.09011.1951-1.17756.7445-0.07070.65250.48460.0518-0.0629-0.0055-0.29750.39670.13370.20720.00180.07340.0847-0.00910.15145.51736.48447.589
3014.16364.13461.964217.5446.78928.63660.5369-0.71920.38541.3486-0.06090.39590.5615-0.1071-0.47590.3612-0.00640.17340.20040.00970.200812.44230.6758.5
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 17
2X-RAY DIFFRACTION2A18 - 25
3X-RAY DIFFRACTION3A26 - 40
4X-RAY DIFFRACTION4A41 - 49
5X-RAY DIFFRACTION5A50 - 58
6X-RAY DIFFRACTION6A59 - 68
7X-RAY DIFFRACTION7A69 - 79
8X-RAY DIFFRACTION8A80 - 99
9X-RAY DIFFRACTION9A100 - 110
10X-RAY DIFFRACTION10A111 - 135
11X-RAY DIFFRACTION11A136 - 148
12X-RAY DIFFRACTION12A149 - 172
13X-RAY DIFFRACTION13A173 - 177
14X-RAY DIFFRACTION14A178 - 187
15X-RAY DIFFRACTION15A188 - 192
16X-RAY DIFFRACTION16B-1 - 5
17X-RAY DIFFRACTION17B6 - 13
18X-RAY DIFFRACTION18B14 - 31
19X-RAY DIFFRACTION19B32 - 38
20X-RAY DIFFRACTION20B39 - 50
21X-RAY DIFFRACTION21B51 - 70
22X-RAY DIFFRACTION22B71 - 87
23X-RAY DIFFRACTION23B88 - 118
24X-RAY DIFFRACTION24B119 - 128
25X-RAY DIFFRACTION25B129 - 145
26X-RAY DIFFRACTION26B146 - 163
27X-RAY DIFFRACTION27B164 - 169
28X-RAY DIFFRACTION28B170 - 177
29X-RAY DIFFRACTION29B178 - 187
30X-RAY DIFFRACTION30B188 - 192

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