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- PDB-6edd: Crystal structure of a GNAT Superfamily PA3944 acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 6edd
TitleCrystal structure of a GNAT Superfamily PA3944 acetyltransferase in complex with CoA (P1 space group)
ComponentsAcetyltransferase PA3944
KeywordsTRANSFERASE / PA3944 / GNAT / acetyltransferase / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology: / Acetyltransferase (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: 1.55 Å
AuthorsCzub, M.P. / Porebski, P.J. / Majorek, K.A. / Satchell, K.J. / Joachimiak, A. / 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: Biochemistry / Year: 2018
Title: A Gcn5-Related N-Acetyltransferase (GNAT) Capable of Acetylating Polymyxin B and Colistin Antibiotics in Vitro.
Authors: Czub, M.P. / Zhang, B. / Chiarelli, M.P. / Majorek, K.A. / Joe, L. / Porebski, P.J. / Revilla, A. / Wu, W. / Becker, D.P. / Minor, W. / Kuhn, M.L.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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)46,15815
Polymers44,1922
Non-polymers1,96613
Water8,485471
1
A: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9887
Polymers22,0961
Non-polymers8926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1708
Polymers22,0961
Non-polymers1,0747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.452, 44.175, 60.125
Angle α, β, γ (deg.)81.880, 73.320, 89.940
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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Protein , 1 types, 2 molecules AB

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


Mass: 22096.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA3944 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q9HX72, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 484 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 ul of 10 mg/ml protein incubated with 5mM CoA and 5 mM colistin 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, ...Details: 0.3 ul of 10 mg/ml protein incubated with 5mM CoA and 5 mM colistin 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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.914
11H, -K, H-L20.086
ReflectionResolution: 1.55→50 Å / Num. obs: 49684 / % possible obs: 96.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.044 / Rrim(I) all: 0.069 / Χ2: 1.423 / Net I/σ(I): 11.7 / Num. measured all: 121370
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.582.10.39724400.7730.3350.5210.7993.5
1.58-1.612.40.3823830.7760.3210.50.85694.1
1.61-1.642.50.31625160.8290.2660.4140.83795.1
1.64-1.672.50.29224200.8540.2460.3830.87195.2
1.67-1.712.50.23524700.8950.1980.3090.90395.4
1.71-1.752.50.21324850.9040.1780.2790.93395.9
1.75-1.792.50.17824610.9340.1490.2330.98895.6
1.79-1.842.50.15125070.9540.1260.1971.02396
1.84-1.892.50.12624320.9640.1050.1651.12696
1.89-1.952.50.11224910.970.0940.1471.45396
1.95-2.022.50.08525200.9820.0710.1121.39996.7
2.02-2.12.50.07324800.9880.060.0951.45796.9
2.1-2.22.50.06424960.990.0530.0831.61397.2
2.2-2.322.50.05925400.9910.0490.0771.77297.4
2.32-2.462.50.05225130.9930.0420.0671.68497.6
2.46-2.652.50.04725250.9940.0380.0611.80397.8
2.65-2.922.50.04325050.9940.0350.0562.03897.7
2.92-3.342.40.03625550.9950.0290.0472.15297.7
3.34-4.212.40.03124600.9970.0250.042.09696.4
4.21-502.40.03424850.9960.0270.0442.50195.7

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Processing

Software
NameClassification
HKL-3000data reduction
HKL-3000data scaling
SCALEPACKdata scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EDV

6edv


Resolution: 1.55→34.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.0202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.019
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2225 4.7 %RANDOM
Rwork0.1656 ---
obs0.167 44683 91.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.32 Å2 / Biso mean: 19.859 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1-11.34 Å25.97 Å22.72 Å2
2---15.22 Å2-1.77 Å2
3---3.88 Å2
Refinement stepCycle: final / Resolution: 1.55→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 130 476 3642
Biso mean--22.9 31.34 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0143360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172859
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6814599
X-RAY DIFFRACTIONr_angle_other_deg1.7311.6716717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.94619.144222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06215491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.491546
X-RAY DIFFRACTIONr_chiral_restr0.0810.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023977
X-RAY DIFFRACTIONr_gen_planes_other0.010.02675
Refine LS restraints NCS

Ens-ID: 1 / Number: 6260 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.554→1.594 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 53 -
Rwork0.201 1129 -
all-1182 -
obs--30.76 %
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)
14.18180.480.15813.1643-2.18773.9929-0.38780.2381-0.3513-0.17970.0087-0.53810.67840.6490.3790.22390.07870.05070.26140.01610.162525.706-2.94961.185
22.201-1.90460.24921.9031-0.02140.79040.17110.2893-0.2474-0.1369-0.1970.2760.0936-0.11440.02590.037-0.02860.00450.2201-0.00520.143912.978-1.87451.205
31.9927-0.8683-1.04670.38330.50342.69270.2130.3385-0.1885-0.1163-0.14880.0786-0.0998-0.0981-0.06430.18070.0054-0.00670.2895-0.0090.18979.1785.99644.816
42.32131.1101-1.2012.8719-0.39371.8458-0.02050.1206-0.0234-0.1166-0.0013-0.10590.11920.10580.02180.01910.00220.00530.12730.00190.069521.7450.42752.936
51.17620.8478-0.57352.2152-0.02030.96080.03170.0448-0.0377-0.00790.0037-0.106-0.01120.0625-0.03530.0041-0.0040.01040.12390.00450.075421.51110.35259.015
61.20660.72460.1553.3912-0.09561.57650.0523-0.00130.02870.0583-0.03970.1498-0.1378-0.133-0.01250.0240.00240.02260.10360.00350.061412.16218.75962.539
71.6406-0.29581.60871.8405-0.43615.7229-0.02760.20150.0691-0.1885-0.0040.1616-0.1467-0.21290.03150.0608-0.00450.02790.12920.00520.091112.92122.25151.329
85.81222.96574.63416.62617.424511.15490.2594-0.87350.32920.6791-0.36110.57580.1437-0.7060.10170.2535-00.14580.27460.02820.283725.75216.25370.961
95.9849-1.7876-4.34357.57463.38936.7624-0.1220.29870.0557-0.4109-0.0432-0.077-0.01840.15530.16520.266-0.0020.00170.34440.03410.263713.56211.27341.24
101.55460.99780.86151.63220.01143.97940.0822-0.16-0.12740.0672-0.00350.16720.3123-0.2828-0.07860.04640.00610.01430.13010.01420.105720.4899.38126.732
113.0860.1471-0.49540.446-0.20061.06510.004-0.13550.09490.1264-0.0138-0.0758-0.04370.12940.00990.0473-0.01430.00240.1690.00960.099627.17718.43434.228
121.1544-0.3158-0.52792.2486-0.97931.6790.0244-0.1030.07110.21060.0126-0.0327-0.08960.0248-0.0370.0256-0.01890.00220.12760.00110.056223.11420.16526.002
138.8076-4.5022-1.94523.04040.94641.2631-0.02080.1896-0.1593-0.06-0.01230.27460.0405-0.22220.0330.0768-0.0106-0.00850.10620.01520.080116.74320.01817.235
142.1674-0.7479-0.22643.8478-0.4341.428-0.0016-0.26630.08870.3990.0108-0.2248-0.2120.1067-0.00920.071-0.02110.00370.1250.01150.08227.833.19223.97
155.28371.26412.50265.2111.57536.16560.0213-0.40320.10710.45670.0012-0.3743-0.04560.1176-0.02260.11050.00860.0180.10710.01080.114326.05435.45924.836
162.2792-3.01875.35636.1327-6.770512.65330.17920.41020.119-0.827-0.381-0.40610.31310.92930.20170.19960.05840.11050.35710.08620.244315.10929.62911.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 17
2X-RAY DIFFRACTION2A18 - 42
3X-RAY DIFFRACTION3A43 - 56
4X-RAY DIFFRACTION4A57 - 85
5X-RAY DIFFRACTION5A86 - 140
6X-RAY DIFFRACTION6A141 - 164
7X-RAY DIFFRACTION7A165 - 185
8X-RAY DIFFRACTION8A186 - 192
9X-RAY DIFFRACTION9B0 - 8
10X-RAY DIFFRACTION10B9 - 32
11X-RAY DIFFRACTION11B33 - 69
12X-RAY DIFFRACTION12B70 - 112
13X-RAY DIFFRACTION13B113 - 134
14X-RAY DIFFRACTION14B135 - 175
15X-RAY DIFFRACTION15B176 - 185
16X-RAY DIFFRACTION16B186 - 192

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