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- PDB-4my3: Crystal Structure of GCN5-related N-acetyltransferase from Kribbe... -

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Basic information

Entry
Database: PDB / ID: 4my3
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
GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 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 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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)255,35610
Polymers255,1616
Non-polymers1954
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22060 Å2
ΔGint-75 kcal/mol
Surface area87340 Å2
MethodPISA
2
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1254
Polymers85,0542
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-34 kcal/mol
Surface area32320 Å2
MethodPISA
3
C: GCN5-related N-acetyltransferase
D: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1784
Polymers85,0542
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-7 kcal/mol
Surface area31840 Å2
MethodPISA
4
E: GCN5-related N-acetyltransferase
F: GCN5-related N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)85,0542
Polymers85,0542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-18 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.246, 167.120, 183.169
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

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M MES pH 6.5, 10 %(w/v) PEG400, 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: 2.57→50 Å / Num. all: 90603 / Num. obs: 90603 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 39.98 Å2 / Rsym value: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 2.57→2.61 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4461 / Rsym value: 0.792 / % possible all: 98.6

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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: 2.57→41.966 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4161 5.04 %random
Rwork0.176 ---
obs0.179 82586 93.96 %-
all-82586 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 2.57→41.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17709 0 10 401 18120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818215
X-RAY DIFFRACTIONf_angle_d1.18424792
X-RAY DIFFRACTIONf_dihedral_angle_d16.1516434
X-RAY DIFFRACTIONf_chiral_restr0.0782696
X-RAY DIFFRACTIONf_plane_restr0.0053280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.57-2.59920.365790.24181485156454
2.5992-2.62980.3493940.24191714180862
2.6298-2.66180.31411070.2452004211173
2.6618-2.69550.33491300.24342253238082
2.6955-2.7310.3381280.24382479260791
2.731-2.76840.30771470.22812621276896
2.7684-2.80790.33831260.23622696282297
2.8079-2.84980.31421510.2282685283698
2.8498-2.89440.27911410.22632720286198
2.8944-2.94180.27921510.22482718286999
2.9418-2.99250.34631400.23352737287799
2.9925-3.04690.29251460.22152700284699
3.0469-3.10550.26431470.20962716286398
3.1055-3.16890.27361420.20262709285198
3.1689-3.23780.27641430.20672688283198
3.2378-3.3130.2461400.20642739287998
3.313-3.39590.26791230.2022762288599
3.3959-3.48760.30171390.2012697283699
3.4876-3.59020.25151570.18832752290999
3.5902-3.7060.21741500.17272750290099
3.706-3.83840.21311620.16422693285599
3.8384-3.9920.22671650.14982736290199
3.992-4.17350.19381490.14272750289999
4.1735-4.39330.18211370.13372778291599
4.3933-4.66820.18191510.12812760291199
4.6682-5.02810.18541490.13162766291599
5.0281-5.53310.191240.14662828295299
5.5331-6.33140.2271360.16542796293298
6.3314-7.9680.19851630.16012813297698
7.968-41.97140.16541440.14532880302496
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)
12.3099-0.82341.48892.85051.01293.22830.13790.7872-0.0785-0.09710.057-0.71710.23720.6657-0.14260.37860.15780.05540.577-0.02620.451748.7077-9.3495-14.3105
20.78780.4823-0.09842.1198-0.23161.32080.1960.0237-0.10460.3563-0.0994-0.2460.12640.2973-0.05050.22650.0122-0.01230.2803-0.00310.186244.02446.071-9.35
32.3683-0.4663-0.60022.4702-0.51412.90880.1271-0.00640.0256-0.1114-0.2289-0.33150.17980.60230.09840.2033-0.03630.03930.410.0490.254453.283420.8354-20.0005
40.7617-0.71790.54841.2844-1.2572.229-0.1546-0.13090.13270.27270.0802-0.1134-0.2416-0.02960.05730.3243-0.064-0.01070.2354-0.01480.176735.702918.20822.7158
50.6810.0901-0.63922.3155-0.89933.1178-0.050.04520.11270.036-0.13080.3268-0.0866-0.60970.09810.1277-0.01370.04020.2587-0.09730.322723.265846.5458-29.7455
63.93552.2024-0.73552.75190.1141.34230.1926-0.18670.40.1975-0.2290.5119-0.1862-0.26940.03220.2847-0.03760.05880.2656-0.06030.257214.223323.6951-12.9897
70.73020.0965-0.29461.6861-0.16080.08560.0653-0.20710.06180.396-0.0798-0.12550.02230.05330.01410.3273-0.0811-0.02750.294-0.01080.159935.543237.1665-10.4322
81.4109-0.72331.02692.3143-0.68872.8769-0.0964-0.11170.09380.0838-0.008-0.6253-0.09480.35410.09270.14350.01230.05740.3343-0.00170.440964.010917.2969-48.2054
91.29851.0711-0.23524.56670.91541.0882-0.0647-0.1665-0.4486-0.143-0.0899-0.58920.1160.16370.12510.27440.08130.00910.19730.04970.327945.21041.0318-63.9806
101.70220.71280.39742.09780.45651.4656-0.2010.02380.2648-0.87470.0067-0.2556-0.54650.2540.13250.69560.04810.01660.20330.04130.315753.148328.807-67.7934
111.79650.8713-0.70282.1279-0.57951.5725-0.0677-0.04820.47950.32150.14040.5228-0.4013-0.609-0.01120.25910.1733-0.05770.4092-0.04760.32515.862420.6252-65.6182
120.63071.0024-0.05161.280.40060.3618-0.1070.06590.0749-0.16860.11570.0612-0.0456-0.04530.00420.24810.0608-0.08430.1727-0.00760.185422.608724.091-66.1636
131.69260.51920.06782.26031.71873.29950.07620.00570.0831-0.1218-0.23180.2556-0.2549-0.29410.10820.19590.043-0.02410.1673-0.03770.243128.669934.8943-55.1899
140.82240.30860.76781.36771.09262.9733-0.09520.12460.0448-0.28210.0601-0.0561-0.19990.13650.02920.25270.04690.00630.1557-0.00250.173633.516518.9552-78.2423
153.4876-0.9246-0.95071.1539-0.32141.4491-0.1135-0.0965-0.0506-0.0002-0.0236-0.1633-0.0344-0.02720.12480.22680.0483-0.0140.1167-0.04050.195636.8059-25.2111-52.3428
160.575-0.04270.8231.61921.00583.82440.03860.0386-0.04430.54160.0459-0.28390.42440.1877-0.05180.33920.0664-0.01590.1993-0.01380.193225.8558-18.2902-27.3186
172.6042-0.62820.31861.9429-0.79861.7486-0.0902-0.1709-0.62040.08230.23570.74830.3347-0.4299-0.04590.1593-0.0274-0.01010.3448-0.01880.42510.7796-32.4182-51.0133
183.83880.7364-1.23253.2613-3.23617.202-0.0667-0.33630.3640.2107-0.48480.1656-0.840.3630.36750.32840.0745-0.00390.4804-0.18390.4344-5.319513.4317-21.6912
191.611-0.43050.33632.42370.78682.00070.0335-0.20810.10270.1922-0.36750.44870.039-0.2960.28350.1616-0.04340.05960.4494-0.09130.3488-5.37610.8945-24.7176
20-0.02150.0917-0.12510.8049-0.34381.83980.11360.11380.1858-0.0811-0.12210.1848-0.1013-0.32380.0050.13250.0775-0.03210.3979-0.06130.23060.0521-5.6044-48.9918
212.8448-0.8004-0.6643.280.19622.21750.08470.12070.4059-0.0445-0.1341-0.0287-0.0397-0.07850.02640.15360.09670.0070.3444-0.02440.13053.7274-1.8697-53.9697
221.5206-0.52580.61081.76240.48910.55540.02950.21230.2005-0.231-0.0404-0.13350.05920.19920.00150.14520.08130.04730.27420.00920.187615.295-6.4208-50.1333
232.4137-0.1887-0.39842.8305-0.61912.27980.0174-0.3486-0.56250.35330.06870.75370.5745-0.5285-0.05040.3927-0.11230.06620.44690.04350.5112-4.9814-22.671-24.7117
242.8951-0.96040.66322.1786-0.1991.3136-0.1201-0.4591-0.45780.45630.16420.0170.5265-0.1352-0.05430.394-0.020.02130.2220.0820.27624.6197-21.36-22.948
251.92890.41810.50820.1746-0.38393.01770.34010.0326-0.47210.293-0.03710.40940.534-0.1239-0.2890.4224-0.0402-0.01790.2908-0.09280.43183.8344-20.9321-30.0412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 389 )
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 131 )
6X-RAY DIFFRACTION6chain 'B' and (resid 132 through 243 )
7X-RAY DIFFRACTION7chain 'B' and (resid 244 through 389 )
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 131 )
9X-RAY DIFFRACTION9chain 'C' and (resid 132 through 263 )
10X-RAY DIFFRACTION10chain 'C' and (resid 264 through 389 )
11X-RAY DIFFRACTION11chain 'D' and (resid 4 through 72 )
12X-RAY DIFFRACTION12chain 'D' and (resid 73 through 178 )
13X-RAY DIFFRACTION13chain 'D' and (resid 179 through 258 )
14X-RAY DIFFRACTION14chain 'D' and (resid 259 through 389 )
15X-RAY DIFFRACTION15chain 'E' and (resid 4 through 131 )
16X-RAY DIFFRACTION16chain 'E' and (resid 132 through 281 )
17X-RAY DIFFRACTION17chain 'E' and (resid 282 through 389 )
18X-RAY DIFFRACTION18chain 'F' and (resid 4 through 30 )
19X-RAY DIFFRACTION19chain 'F' and (resid 31 through 131 )
20X-RAY DIFFRACTION20chain 'F' and (resid 132 through 197 )
21X-RAY DIFFRACTION21chain 'F' and (resid 198 through 242 )
22X-RAY DIFFRACTION22chain 'F' and (resid 243 through 272 )
23X-RAY DIFFRACTION23chain 'F' and (resid 273 through 337 )
24X-RAY DIFFRACTION24chain 'F' and (resid 338 through 360 )
25X-RAY DIFFRACTION25chain 'F' and (resid 361 through 389 )

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