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- PDB-7kpp: Structure of the E102A mutant of a GNAT superfamily PA3944 acetyl... -

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Basic information

Entry
Database: PDB / ID: 7kpp
TitleStructure of the E102A mutant of a GNAT superfamily PA3944 acetyltransferase
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 / COENZYME A / Acetyltransferase PA3944
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCzub, M.P. / Porebski, P.J. / Majorek, K.A. / Cymborowski, M. / 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 1.1Aug 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 1.2Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,04619
Polymers44,0762
Non-polymers1,97017
Water10,521584
1
A: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,11613
Polymers22,0381
Non-polymers1,07812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9306
Polymers22,0381
Non-polymers8925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.344, 44.038, 60.184
Angle α, β, γ (deg.)98.030, 106.880, 90.030
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: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 9 - 191 / Label seq-ID: 11 - 193

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

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Components

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


Mass: 22038.008 Da / Num. of mol.: 2 / Mutation: E102A
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: 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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 uL of 10 mg/mL protein incubated with 5mM 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 10 mg/mL protein incubated with 5mM 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).

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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 210r / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 60281 / % possible obs: 96.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.024 / Rrim(I) all: 0.052 / Χ2: 0.973 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.4840.20629220.9380.1190.240.87393.1
1.48-1.54.30.18729040.9560.1030.2150.9293.6
1.5-1.534.70.1829460.9680.0930.2030.93594.4
1.53-1.564.80.15829790.9770.080.1780.89994.8
1.56-1.64.80.13929850.9840.070.1560.994.9
1.6-1.634.80.12430130.9850.0630.1390.93295.4
1.63-1.674.80.1129640.9880.0560.1240.90595.4
1.67-1.724.80.09729840.990.0490.1090.97195.5
1.72-1.774.80.08930190.9910.0450.10.95195.8
1.77-1.834.80.07830120.9940.0390.0880.98396.3
1.83-1.894.80.06730340.9940.0340.0750.9896.3
1.89-1.974.80.05829800.9950.0290.0651.01696.4
1.97-2.064.80.05130220.9970.0260.0581.04996.8
2.06-2.174.80.04630680.9970.0230.0521.03997.2
2.17-2.34.80.04230600.9970.0210.0471.00397.4
2.3-2.484.80.0430700.9980.020.0450.99897.8
2.48-2.734.80.03730840.9980.0190.0421.00798.1
2.73-3.124.80.03430610.9980.0170.0381.00398.5
3.12-3.944.80.03131010.9980.0160.0350.98498.9
3.94-504.70.03530950.9960.0180.041.06698.7

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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: 1.45→43.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.811 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 2930 4.9 %RANDOM
Rwork0.1487 ---
obs0.1496 57351 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 17.049 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.01 Å2-0.06 Å2
2---0.24 Å20.04 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.45→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 0 132 588 3755
Biso mean--18.46 28.55 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133324
X-RAY DIFFRACTIONr_bond_other_d0.0070.0173040
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.6634535
X-RAY DIFFRACTIONr_angle_other_deg1.3711.5766959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.14218.655223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35515484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.281547
X-RAY DIFFRACTIONr_chiral_restr0.0690.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02873
Refine LS restraints NCS

Ens-ID: 1 / Number: 6178 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 189 -
Rwork0.187 4098 -
all-4287 -
obs--92.95 %
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)
10.7911-0.37981.33861.3467-0.54176.2565-0.0097-0.06020.1068-0.01570.01870.0837-0.0934-0.419-0.00890.04710.00050.01320.0935-0.00190.0696-3.92518.32220.138
23.144-2.33940.6351.8261-0.36540.74210.03390.15410.1626-0.0321-0.0782-0.1382-0.05860.03260.04430.01790.00060.01420.06690.01970.05459.73815.4138.943
33.3303-0.3847-0.02320.2887-0.1590.48840.04440.30750.0465-0.0476-0.0406-0.01420.02640.0064-0.00390.02770.00130.01520.08490.00810.03524.24110.5423.844
40.18330.10340.24551.8329-0.20590.54240.02280.01570.0045-0.0179-0.0348-0.05620.0006-0.03240.01210.01790.0070.01460.0554-0.00710.0405-0.8458.42313.543
51.43930.76950.45730.96030.16390.69570.0422-0.02110.01270.0535-0.0368-0.0051-0.009-0.0002-0.00540.00420.00130.0030.03010.00240.04213.139.24920.72
65.068-0.9883-1.14510.9170.34870.591-0.0080.00130.0271-0.0017-0.01830.06490.0272-0.02560.02630.0053-0.00550.00430.04990.00510.0411-4.0360.71319.167
70.6689-0.0926-0.03120.7362-0.01960.87180.01860.0644-0.0063-0.0203-0.0005-0.03710.08440.031-0.0180.00940.00490.00150.04920.00120.0337.091-5.23516.609
86.71260.7933-2.87612.9877-4.59017.48620.12-0.3894-0.12120.3592-0.2922-0.1038-0.55030.4940.17230.1377-0.0542-0.02390.15130.02830.0623-5.604-0.36330.602
92.84490.3794.51160.05150.62018.81120.0614-0.4453-0.04640.001-0.0498-0.0009-0.0791-0.6076-0.01160.1733-0.0416-0.00510.19610.01670.156224.88538.31960.117
100.70580.00460.04830.63350.19631.160.0232-0.07370.0684-0.0039-0.0468-0.0057-0.09340.05510.02370.0140.00480.00490.0543-0.00520.03814.37338.76444.44
113.0049-0.06030.25870.08290.28681.0885-0.0165-0.196-0.04430.0214-0.00370.00410.0662-0.07190.02020.03190.00410.01420.08150.00110.030412.54732.92253.795
120.23950.35740.38390.9190.7791.11390.0615-0.0475-0.00980.0390.0049-0.02180.09420.0337-0.06640.0285-0.01060.00640.06130.00410.042220.23130.35543.996
131.474-0.61480.33220.96760.10870.66340.03510.05010.0142-0.042-0.0158-0.0433-0.00950.0302-0.01920.0036-0.00480.00720.0338-0.00340.036418.76430.47235.611
140.5480.04980.08951.54410.41870.78890.0359-0.0266-0.00330.0658-0.04120.09860.0944-0.05750.00520.0128-0.00840.00340.0444-0.00540.042111.52218.53536.194
151.26010.1068-0.62452.1-0.17541.83460.0691-0.1979-0.06360.4643-0.00110.13970.0951-0.0237-0.06790.1215-0.02080.02270.06980.0070.033811.77715.3245.551
164.1123-2.4882-4.42376.36026.07947.17090.17480.3688-0.1005-0.5231-0.44010.3088-0.4832-0.48430.26530.14250.0552-0.05430.207-0.05160.096923.78421.99626.371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 21
2X-RAY DIFFRACTION2A22 - 43
3X-RAY DIFFRACTION3A44 - 66
4X-RAY DIFFRACTION4A67 - 98
5X-RAY DIFFRACTION5A99 - 128
6X-RAY DIFFRACTION6A129 - 144
7X-RAY DIFFRACTION7A145 - 186
8X-RAY DIFFRACTION8A187 - 192
9X-RAY DIFFRACTION9B0 - 5
10X-RAY DIFFRACTION10B6 - 43
11X-RAY DIFFRACTION11B44 - 63
12X-RAY DIFFRACTION12B64 - 100
13X-RAY DIFFRACTION13B101 - 136
14X-RAY DIFFRACTION14B137 - 165
15X-RAY DIFFRACTION15B166 - 187
16X-RAY DIFFRACTION16B188 - 192

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