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- PDB-4my0: Crystal Structure of GCN5-related N-acetyltransferase from Kribbe... -

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Basic information

Entry
Database: PDB / ID: 4my0
TitleCrystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta structure
Function / homology
Function and homology information


aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity
Similarity search - Function
Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Acetyltransferase (GNAT) domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) ...Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Acetyltransferase (GNAT) domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AC8 / ACETYL COENZYME *A / GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.101 Å
AuthorsKim, Y. / Mack, J. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida
Authors: Kim, Y. / Mack, J. / Endres, M. / Joachimiak, A.
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
C: GCN5-related N-acetyltransferase
D: GCN5-related N-acetyltransferase
E: GCN5-related N-acetyltransferase
F: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,97420
Polymers255,1616
Non-polymers5,81214
Water12,827712
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0097
Polymers85,0542
Non-polymers1,9565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-20 kcal/mol
Surface area30640 Å2
MethodPISA
3
C: GCN5-related N-acetyltransferase
D: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9556
Polymers85,0542
Non-polymers1,9014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-13 kcal/mol
Surface area31080 Å2
MethodPISA
4
E: GCN5-related N-acetyltransferase
F: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0097
Polymers85,0542
Non-polymers1,9565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-19 kcal/mol
Surface area31280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.138, 166.518, 183.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailshexamer as in the asymmetric unit

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
GCN5-related N-acetyltransferase


Mass: 42526.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_4406 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D2PVF8

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Non-polymers , 5 types, 726 molecules

#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AC8 / [(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-bis(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl dihydrogen diphosphate


Mass: 847.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H37N7O19P4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE AUTHOR STATES THAT THE N-TERMINAL SER ASN ALA ARE CLONING ARTIFACTS THAT ARE RESIDUAL OF THE ...THE AUTHOR STATES THAT THE N-TERMINAL SER ASN ALA ARE CLONING ARTIFACTS THAT ARE RESIDUAL OF THE CLEAVED HIS-TAG AND VAL IS AN EXPRESSION ARTIFACT.

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 16 %(w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 163672 / Num. obs: 163672 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 28.48 Å2 / Rsym value: 0.097 / Net I/σ(I): 7.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 7869 / Rsym value: 0.625 / % possible all: 96.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.101→36.909 Å / SU ML: 0.21 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.202 8198 5.02 %random
Rwork0.1663 ---
obs0.168 163379 99.24 %-
all-163379 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.1 Å2
Refinement stepCycle: LAST / Resolution: 2.101→36.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17731 0 352 712 18795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818584
X-RAY DIFFRACTIONf_angle_d1.24925342
X-RAY DIFFRACTIONf_dihedral_angle_d16.346600
X-RAY DIFFRACTIONf_chiral_restr0.1092742
X-RAY DIFFRACTIONf_plane_restr0.0043307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1005-2.12440.25242270.22884391461886
2.1244-2.14940.27612840.2215012529697
2.1494-2.17560.27442830.21495029531298
2.1756-2.20310.25372610.21225113537499
2.2031-2.23210.25933030.206151255428100
2.2321-2.26270.25772890.214151695458100
2.2627-2.2950.25442680.196451505418100
2.295-2.32920.25132520.189351425394100
2.3292-2.36560.22922620.188552465508100
2.3656-2.40440.23012690.188151145383100
2.4044-2.44590.22512720.187852295501100
2.4459-2.49030.24132790.19151755454100
2.4903-2.53820.22522890.190751355424100
2.5382-2.590.23092710.18951655436100
2.59-2.64630.25092650.187752135478100
2.6463-2.70780.23592800.183751875467100
2.7078-2.77550.24152790.186651795458100
2.7755-2.85060.24472550.196951965451100
2.8506-2.93440.21542550.187952315486100
2.9344-3.02910.2432750.192352085483100
3.0291-3.13730.21852850.180251825467100
3.1373-3.26280.22282490.180952635512100
3.2628-3.41120.21532790.173252145493100
3.4112-3.59090.19742760.160852185494100
3.5909-3.81570.18112730.147552615534100
3.8157-4.110.16252740.135152475521100
4.11-4.52290.14422840.12552705554100
4.5229-5.17580.16142610.124553345595100
5.1758-6.51520.16692890.151953505639100
6.5152-36.91440.15763100.14255433574398
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)
12.2738-0.9834-0.8981.52980.70541.42490.018-0.15240.20780.1180.1197-0.5014-0.21670.2905-0.12450.2792-0.0739-0.11950.2534-0.01130.331534.746519.229766.5842
20.50030.02080.56311.2505-1.05412.49360.0207-0.07640.01840.3101-0.0256-0.0578-0.1834-0.01170.00790.23170.0116-0.02850.1786-0.00270.175613.01426.710166.0008
30.95050.36980.64661.11320.30392.1669-0.0179-0.065-0.01090.11930.08970.3440.0834-0.4156-0.03030.14720.02240.06770.32590.09210.3345-19.630413.862250.8209
41.0933-0.7438-0.24612.6808-0.04950.8721-0.017-0.05020.04090.41810.03060.1491-0.14-0.1642-0.0070.24030.00850.01640.2167-0.00150.1446-2.946912.203666.5606
50.86310.23640.02131.1060.19723.1469-0.06730.07720.1375-0.1072-0.0103-0.1513-0.29110.30550.06620.2058-0.0187-0.00730.2170.07950.249916.508444.054427.4553
61.4388-0.96580.07651.8431-0.30250.3615-0.05830.19610.0398-0.29380.0213-0.02090.0286-0.07020.03410.283-0.04270.01050.27210.03960.148613.211628.39189.9902
71.0805-0.75740.44771.8898-0.62370.89010.06690.0598-0.2577-0.5930.15380.48480.3394-0.3582-0.17150.5133-0.1581-0.14630.40420.01460.298-2.9541-6.33058.1018
81.0336-0.013-0.50240.88840.1351.7859-0.00160.2780.0692-0.37630.06530.15850.1385-0.277-0.06580.3378-0.0605-0.08990.32910.090.2309-4.693716.450110.5114
91.5108-0.3660.14031.3316-0.52921.0015-0.04170.0950.1163-0.3021-0.1182-0.75210.04870.28080.13810.2679-0.00050.20.32660.02570.537247.37214.338220.5377
102.310.6113-0.34641.35920.98731.99110.0099-0.13190.0133-0.00740.0794-0.46390.02940.3751-0.06870.15220.0078-0.00010.2760.03150.405444.1765-1.955247.6858
111.0466-0.0236-0.29320.9680.20841.5905-0.03680.1884-0.2958-0.1554-0.076-0.42420.38630.09450.08020.27620.03620.11680.2294-0.00190.522642.0928-16.705430.309
122.2762-0.0986-0.82062.05960.60591.6749-0.13390.0061-0.26590.092-0.06630.06550.2269-0.07970.19330.2188-0.04550.01420.13080.00150.16718.2874-26.310652.4983
130.39420.13370.35141.26-0.81772.3332-0.03030.0961-0.126-0.36280.0806-0.06850.3165-0.005-0.04920.2425-0.03510.06850.1975-0.02340.220618.8535-19.674128.3122
141.4843-0.18290.18391.6719-0.2131.4374-0.08010.0032-0.33910.0692-0.0041-0.78020.26310.32580.05070.25230.06070.01050.25960.03290.591435.3537-30.208148.2545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 134 )
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 389 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 134 )
4X-RAY DIFFRACTION4chain 'B' and (resid 135 through 389 )
5X-RAY DIFFRACTION5chain 'C' and (resid -2 through 134 )
6X-RAY DIFFRACTION6chain 'C' and (resid 135 through 389 )
7X-RAY DIFFRACTION7chain 'D' and (resid 4 through 134 )
8X-RAY DIFFRACTION8chain 'D' and (resid 135 through 389 )
9X-RAY DIFFRACTION9chain 'E' and (resid 4 through 134 )
10X-RAY DIFFRACTION10chain 'E' and (resid 135 through 229 )
11X-RAY DIFFRACTION11chain 'E' and (resid 230 through 389 )
12X-RAY DIFFRACTION12chain 'F' and (resid 3 through 110 )
13X-RAY DIFFRACTION13chain 'F' and (resid 111 through 272 )
14X-RAY DIFFRACTION14chain 'F' and (resid 273 through 389 )

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