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- PDB-2ozg: Crystal structure of GCN5-related N-acetyltransferase (YP_325469.... -

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Basic information

Entry
Database: PDB / ID: 2ozg
TitleCrystal structure of GCN5-related N-acetyltransferase (YP_325469.1) from Anabaena variabilis ATCC 29413 at 2.00 A resolution
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / YP_325469.1 / GCN5-related N-acetyltransferase / Acetyltransferase (GNAT) family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Acetyltransferase (GNAT) domain / SCP2 sterol-binding 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 / Acetyltransferase (GNAT) domain / SCP2 sterol-binding 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
ACETATE ION / COENZYME A / DI(HYDROXYETHYL)ETHER / GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of GCN5-related N-acetyltransferase (YP_325469.1) from Anabaena variabilis ATCC 29413 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0357
Polymers44,7841
Non-polymers1,2516
Water4,756264
1
A: GCN5-related N-acetyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)276,21042
Polymers268,7046
Non-polymers7,50636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
MethodPQS
2
A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,07014
Polymers89,5682
Non-polymers2,50212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8360 Å2
ΔGint12 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.965, 174.965, 71.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein GCN5-related N-acetyltransferase


Mass: 44783.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: PCC 7937 / Gene: YP_325469.1, Ava_4977 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q3M362, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: NANODROP, 0.2M K3 Citrate, 20% PEG 3350, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381, 0.979310, 0.978835
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2007
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.979311
30.9788351
ReflectionResolution: 2→29.161 Å / Num. obs: 28396 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 30.89 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.054.60.7311.1943520630.73199.6
2.05-2.114.80.5681.3981620430.56899.7
2.11-2.174.90.4511.7961919610.45199.6
2.17-2.2450.4191.8958019260.41999.6
2.24-2.314.90.3592.1922418700.35999.9
2.31-2.395.10.2632.9921117890.26399.9
2.39-2.485.20.243.2914417540.24100
2.48-2.585.30.1794.2888016780.179100
2.58-2.75.30.1654.5850715970.165100
2.7-2.835.40.1335.5832815520.133100
2.83-2.985.40.116.5786614660.11100
2.98-3.165.30.0897.8744013930.089100
3.16-3.385.30.0699.5701313150.069100
3.38-3.655.30.0610.9643912220.06100
3.65-45.20.05211.9596411380.052100
4-4.475.30.04613.6533610100.046100
4.47-5.165.10.05710.646149100.057100
5.16-6.3250.0698.638397710.069100
6.32-8.945.10.04314.230526020.043100
8.94-29.164.60.03716.115483360.03796.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.161 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.822 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.156
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. COENZYME A WAS MODELED IN THE STRUCTURE BASED ON PROPOSED FUNCTION. 5. ONE ACETATE ION WAS MODELED IN THE STRUCTURE. 6. FOUR POLYETHYLENE GLYCOL MOLECULES FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 7. RESIDUES 1 TO 7 ARE DISORDERED AND WERE NOT BUILT IN THIS MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1437 5.1 %RANDOM
Rwork0.161 ---
all0.164 ---
obs0.164 28395 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.152 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.52 Å20 Å2
2---1.03 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2→29.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 80 264 3384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223237
X-RAY DIFFRACTIONr_bond_other_d0.0010.022941
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9744405
X-RAY DIFFRACTIONr_angle_other_deg0.84336832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3815399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46724.653144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90515530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5721517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023587
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02633
X-RAY DIFFRACTIONr_nbd_refined0.2140.3604
X-RAY DIFFRACTIONr_nbd_other0.1870.33128
X-RAY DIFFRACTIONr_nbtor_refined0.1850.51598
X-RAY DIFFRACTIONr_nbtor_other0.0940.51966
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.5402
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.329
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.371
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.533
X-RAY DIFFRACTIONr_mcbond_it2.56832119
X-RAY DIFFRACTIONr_mcbond_other0.6693803
X-RAY DIFFRACTIONr_mcangle_it3.44653166
X-RAY DIFFRACTIONr_scbond_it5.66181419
X-RAY DIFFRACTIONr_scangle_it7.491111238
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 105 -
Rwork0.225 1957 -
obs-2062 99.37 %
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)
12.7340.9217-0.31511.7765-0.10160.39740.1571-0.29730.13470.2908-0.15460.2129-0.0315-0.1083-0.00250.0152-0.03640.0241-0.0225-0.0694-0.1026-3.643430.333422.9017
20.8143-0.55450.06811.8848-0.15930.6026-0.0258-0.0580.06820.114-0.0136-0.062-0.01110.00750.0394-0.0684-0.0321-0.0171-0.1062-0.0194-0.117616.097827.136611.3279
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
118 - 1309 - 131
22131 - 395132 - 396

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