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

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Basic information

Entry
Database: PDB / ID: 7kps
TitleStructure of a GNAT superfamily PA3944 acetyltransferase in complex with AcCoA
Components(Acetyltransferase ...) x 2
KeywordsTRANSFERASE / PA3944 / acetyltransferase / GNAT Superfamily / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 (GNAT) domain / 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 / COENZYME A / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetyltransferase PA3944
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCzub, M.P. / Porebski, P.J. / Cymborowski, M. / 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: Front Mol Biosci / Year: 2021
Title: Gcn5-Related N- Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too.
Authors: Baumgartner, J.T. / Habeeb Mohammad, T.S. / Czub, M.P. / Majorek, K.A. / Arolli, X. / Variot, C. / Anonick, M. / Minor, W. / Ballicora, M.A. / Becker, D.P. / Kuhn, M.L.
History
DepositionNov 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Structure summary / Category: audit_author
Revision 1.2Aug 9, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)46,60813
Polymers44,1762
Non-polymers2,43211
Water5,170287
1
A: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1726
Polymers22,0961
Non-polymers1,0765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4367
Polymers22,0801
Non-polymers1,3566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.563, 44.246, 60.183
Angle α, β, γ (deg.)97.940, 106.720, 89.920
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 9 - 191 / Label seq-ID: 11 - 193

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

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Components

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Acetyltransferase ... , 2 types, 2 molecules AB

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


Mass: 22096.045 Da / Num. of mol.: 1
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
#2: Protein Acetyltransferase PA3944 / GCN5-related N-acetyltransferase / GNAT


Mass: 22080.045 Da / Num. of mol.: 1
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 , 7 types, 298 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 uL of 10 mg/mL protein incubated with 5mM AcCoA and 5 mM (R)-3-(2-chloroacetamido)-4-(((S)-1-methoxy-1-oxo-3-phenylpropan-2-yl)amino)-4-oxobutanoic acid was mixed with 0.2 uL of the well ...Details: 0.3 uL of 10 mg/mL protein incubated with 5mM AcCoA and 5 mM (R)-3-(2-chloroacetamido)-4-(((S)-1-methoxy-1-oxo-3-phenylpropan-2-yl)amino)-4-oxobutanoic acid 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).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2017
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, L10.851
11H, -K, -H-L20.149
ReflectionResolution: 1.8→50 Å / Num. obs: 32365 / % possible obs: 97.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.068 / Rrim(I) all: 0.102 / Χ2: 0.737 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.831.90.59216090.5530.5490.8090.68695.6
1.83-1.8620.54615800.5450.5040.7450.76895.7
1.86-1.92.10.48116180.5980.4370.6520.79896.6
1.9-1.942.20.41716140.6360.3760.5630.7796.3
1.94-1.982.20.33915740.7660.3070.4590.8596.8
1.98-2.032.20.30216610.7850.2740.4090.9196.9
2.03-2.082.20.27315790.830.2450.3680.91596.9
2.08-2.132.20.21916460.8780.1980.2960.87697.1
2.13-2.22.20.18716110.8920.1690.2530.87697.2
2.2-2.272.20.16716070.920.1510.2260.85597.7
2.27-2.352.20.15416330.9170.1390.2080.84497.4
2.35-2.442.20.12816400.930.1160.1730.78897.6
2.44-2.552.20.10915990.960.0980.1470.75798
2.55-2.692.20.08916340.9690.080.1210.7197.9
2.69-2.862.20.07416560.9660.0650.0990.67898.1
2.86-3.082.20.05816420.9730.0520.0780.66298.4
3.08-3.392.20.0416420.9890.0360.0540.53898.4
3.39-3.882.20.03315580.9890.0290.0450.51794.9
3.88-4.882.20.02916030.9910.0250.0380.44896
4.88-502.20.02716590.9850.0230.0350.46598.9

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Processing

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

6edd


Resolution: 1.8→37.43 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.683 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1392 4.7 %RANDOM
Rwork0.2064 ---
obs0.2078 28223 89.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.1 Å2 / Biso mean: 24.695 Å2 / Biso min: 10.02 Å2
Baniso -1Baniso -2Baniso -3
1-5.91 Å21.39 Å23.09 Å2
2---6.6 Å2-0.33 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.8→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 152 287 3414
Biso mean--29.45 30.82 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133228
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172955
X-RAY DIFFRACTIONr_angle_refined_deg1.181.664387
X-RAY DIFFRACTIONr_angle_other_deg1.1081.5776753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5035371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.81918.826213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29115462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3741544
X-RAY DIFFRACTIONr_chiral_restr0.050.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02831
Refine LS restraints NCS

Ens-ID: 1 / Number: 5937 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.318 21 -
Rwork0.233 467 -
obs--19.54 %
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)
11.5906-0.42610.43490.9807-0.49131.72520.11340.31410.0845-0.2322-0.1006-0.0757-0.01420.0456-0.01270.0999-0.0264-0.01110.20250.01150.16866.01715.3869.742
20.39890.1380.19741.6982-0.34590.90170.02330.0669-0.0219-0.0304-0.01150.01560.0252-0.0185-0.01180.0141-0.0228-0.02590.1378-0.00270.09982.1954.62316.638
38.1123-1.7669-4.2743.93831.34264.88480.0493-0.20670.06750.17570.0408-0.0139-0.0660.1004-0.090.0682-0.028-0.06450.05860.02440.07981.193-3.6321.627
41.99260.6965-0.58571.6553-0.04983.22140.0655-0.23760.04010.126-0.09220.0294-0.05610.03780.02680.04810.0136-0.02870.12320.00210.110713.13338.20646.104
50.6676-0.020.21281.81480.94241.34580.026-0.09-0.06780.1201-0.00040.00280.12520.0163-0.02550.0269-0.0244-0.02910.13010.01230.089417.35427.43740.991
65.80590.8032-2.45525.1381-0.42794.01850.10160.06710.03830.15290.01770.2363-0.0587-0.2079-0.11930.06440.0042-0.07140.0882-0.01040.12316.73618.29637.033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 61
2X-RAY DIFFRACTION2A62 - 175
3X-RAY DIFFRACTION3A176 - 192
4X-RAY DIFFRACTION4B8 - 53
5X-RAY DIFFRACTION5B54 - 173
6X-RAY DIFFRACTION6B174 - 192

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