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- PDB-7q3a: Crystal structure of MAB_4324 a tandem repeat GNAT from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 7q3a
TitleCrystal structure of MAB_4324 a tandem repeat GNAT from Mycobacterium abscessus
ComponentsPutative acetyltransferase, GNAT
KeywordsTRANSFERASE / N-acetyltransferase / acetyl-CoA
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / nucleotide binding
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / ACETATE ION / COENZYME A / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / Acetyltransferase, GNAT
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBlaise, M. / Alsarraf, M.A.B.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Febs Lett. / Year: 2022
Title: Biochemical, structural, and functional studies reveal that MAB_4324c from Mycobacterium abscessus is an active tandem repeat N-acetyltransferase.
Authors: Alsarraf, H.M.A.B. / Ung, K.L. / Johansen, M.D. / Dimon, J. / Olieric, V. / Kremer, L. / Blaise, M.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyltransferase, GNAT
B: Putative acetyltransferase, GNAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,45413
Polymers78,3402
Non-polymers5,11411
Water15,493860
1
A: Putative acetyltransferase, GNAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6486
Polymers39,1701
Non-polymers2,4785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative acetyltransferase, GNAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8067
Polymers39,1701
Non-polymers2,6366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.960, 149.960, 183.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative acetyltransferase, GNAT


Mass: 39170.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: MAB_4324c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1MJN9

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Non-polymers , 8 types, 871 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 3.8 Å3/Da / Density % sol: 67.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M Ammonium sulphate, 0.1 M HEPES pH 7.5 and 2% w/v polyethylene glycol (PEG) 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 80802 / % possible obs: 98.3 % / Redundancy: 38.3 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 1 / Rrim(I) all: 0.1 / Net I/σ(I): 37.4
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 8058 / CC1/2: 0.95 / Rrim(I) all: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.09 Å / SU ML: 0.1773 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.02
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 1969 2.47 %
Rwork0.1862 77651 -
obs0.1871 79620 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.62 Å2
Refinement stepCycle: LAST / Resolution: 2→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 0 323 867 6568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845916
X-RAY DIFFRACTIONf_angle_d0.99388119
X-RAY DIFFRACTIONf_chiral_restr0.0838851
X-RAY DIFFRACTIONf_plane_restr0.00891038
X-RAY DIFFRACTIONf_dihedral_angle_d14.2632062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.24821420.18325615X-RAY DIFFRACTION99.97
2.05-2.110.21511440.1815642X-RAY DIFFRACTION99.98
2.11-2.170.21311420.18055639X-RAY DIFFRACTION100
2.17-2.240.24611260.23154955X-RAY DIFFRACTION87.47
2.24-2.320.323970.26963897X-RAY DIFFRACTION69.1
2.32-2.410.22941450.17685664X-RAY DIFFRACTION100
2.41-2.520.22261430.17415666X-RAY DIFFRACTION99.98
2.52-2.650.23071440.18075688X-RAY DIFFRACTION100
2.65-2.820.21711450.18825709X-RAY DIFFRACTION99.98
2.82-3.040.22341450.19555723X-RAY DIFFRACTION99.98
3.04-3.340.23641470.18335743X-RAY DIFFRACTION100
3.34-3.830.21961460.1875753X-RAY DIFFRACTION99.38
3.83-4.820.20531470.15985823X-RAY DIFFRACTION99.58
4.82-49.090.22651560.19556134X-RAY DIFFRACTION99.92
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)
11.93047638920.205462797577-0.1558005539031.52863441585-0.1018622955451.573141605910.0220981567817-0.0409215686206-0.108241067010.178926133874-0.003862516807870.14791622230.0407515001842-0.137194090013-0.03490749598010.1900304867510.002652594677560.006988981996340.2384969226070.01268123091320.169337040586-11.541117205266.127714335411.7204753073
22.28854681828-0.4768252697970.5840995233651.96987450333-0.6649430115872.2396385669-0.0223481543558-0.0578619624009-0.1175893721160.1488390777440.008698434732020.01332611600880.0589315164277-0.04747489874440.01144850237550.178367907637-0.003945460753710.02366192255340.192903431981-0.006414643090280.143089862947-10.4836323868.31899598317.92937367
32.06032421472-0.828692620642-0.6195034637340.8284141658980.11558190360.460645360274-0.094402234328-0.0174851256384-0.1445762164530.1287582357560.006986899095980.02508573727190.0541497004311-0.008766548573770.09073565316820.166299992918-0.0216338544433-0.02012304743220.2178478140430.006192562034230.188452527919.7864544744857.067546155815.4618877175
42.07996019724-0.7948633803570.2095639109913.54837181221-1.576135194663.07184614003-0.0643997614669-0.136640785331-0.2928517490520.1564599767160.1307103126340.1110951156980.100419743667-0.0472667471121-0.08365753063450.1114207202070.009219751222750.02011911707480.1919614116670.02363129172750.20052767067714.932090738655.007966321912.5602873742
52.3202650677-0.821172624057-0.8327981239320.7121348172040.3437575035641.09411728701-0.0634646298457-0.117162819380.1902031399680.1216854068760.0566766714563-0.2156506904580.07847903718590.131130525-0.01493468385580.195420662842-0.000372389115051-0.03792052906980.2208418015280.002641451512380.22539725936616.204702673663.637997160215.2803104174
62.25183768937-0.3494880189840.03103007709791.146858726580.339380048431.41356574821-0.0707627130890.10873121472-0.178335250328-0.1030331901710.0750351858008-0.2798321181510.0626474110930.3806411818610.0002794175406830.159404219040.01500700092540.03015101383720.300632192655-0.01414540032530.20940437380218.258209219964.646078766-18.5684071341
73.228476882290.0432267521138-0.5014688447454.647191527972.059272751563.29187157594-0.1259052164470.440920439149-0.323403872504-0.09174623610720.096513999252-0.177757105410.2494855958850.232807550228-0.008195639952930.2040321375580.01011629122080.0334893114710.2802988613590.001587573051170.15225698730114.559534172164.9927456086-28.7399383194
82.795982740670.58538843934-0.5894186185530.838134497829-0.1791745312420.803845031158-0.1500129067560.0869813052894-0.274254861101-0.1556755832570.074213854632-0.1666232855310.06499595565260.1049777703270.06990969788780.1898848735430.003021614085390.008847018443680.208384517104-0.02989881632680.183629574312-4.828117180558.2648666702-23.6564070349
91.732706968821.708418355330.05614237830398.379337428872.117617490052.22375956256-0.146520522988-0.00380318376687-0.890569418067-0.1995063541050.1216676074570.1251337452010.1677695400660.07409798695780.02231583694070.1524792272920.028330793460.03918897982580.2075730166560.01959943266730.39943926661-10.627468377547.5492715798-16.1127247218
102.271118219020.533419449952-0.07146691009560.831431042441-0.2581996788840.783807005859-0.06089830585910.0787262357187-0.159143012148-0.1124507191340.0405781605694-0.003117867224240.06962386051960.01518359738970.0270095543140.1579527075310.006665611104270.006966451714480.169272810685-0.009896455519550.164789145527-10.416352017261.4783982217-20.8893020842
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 77 )AA11 - 771 - 67
22chain 'A' and (resid 78 through 160 )AA78 - 16068 - 150
33chain 'A' and (resid 161 through 252 )AA161 - 252151 - 242
44chain 'A' and (resid 253 through 297 )AA253 - 297243 - 284
55chain 'A' and (resid 298 through 352 )AA298 - 352285 - 339
66chain 'B' and (resid 12 through 100 )BE12 - 1001 - 89
77chain 'B' and (resid 101 through 160 )BE101 - 16090 - 149
88chain 'B' and (resid 161 through 238 )BE161 - 238150 - 227
99chain 'B' and (resid 239 through 258 )BE239 - 258228 - 246
1010chain 'B' and (resid 259 through 352 )BE259 - 352247 - 340

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