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- PDB-2pc1: Crystal structure of acetyltransferase GNAT family (NP_688560.1) ... -

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Basic information

Entry
Database: PDB / ID: 2pc1
TitleCrystal structure of acetyltransferase GNAT family (NP_688560.1) from Streptococcus agalactiae 2603 at 1.28 A resolution
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / NP_688560.1 / acetyltransferase GNAT family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyN-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / Acetyltransferase, GNAT family
Function and homology information
Biological speciesStreptococcus agalactiae 2603V/R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.28 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of acetyltransferase GNAT family (NP_688560.1) from Streptococcus agalactiae 2603 at 1.28 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9664
Polymers23,6821
Non-polymers2843
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.480, 37.650, 41.500
Angle α, β, γ (deg.)94.220, 109.420, 113.080
Int Tables number1
Space group name H-MP1
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Acetyltransferase, GNAT family /


Mass: 23681.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae 2603V/R (bacteria)
Species: Streptococcus agalactiae / Strain: 2603 V/R / Gene: NP_688560.1, SAG1567 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q8DYC0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.79
Details: NANODROP, 1.91M Ammonium sulfate, 0.1M Tris-HCl pH 7.79, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 15, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979391
ReflectionResolution: 1.28→25.959 Å / Num. obs: 73297 / % possible obs: 78.3 % / Biso Wilson estimate: 13.84 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 9.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.28-1.330.4221.622396249928.2
1.33-1.380.3512.23324339638.6
1.38-1.440.2662.94788491754.9
1.44-1.520.213.67986797182
1.52-1.610.14357984804989.4
1.61-1.740.09778942892291.8
1.74-1.910.06110.18236838892.7
1.91-2.190.036158796892593.9
2.190.02818.68610884094.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.28→25.959 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.712 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.054
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. SO4 AND GLYCEROL WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1905 5.1 %RANDOM
Rwork0.167 ---
all0.167 ---
obs0.167 37027 79.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.664 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20.16 Å2-0.05 Å2
2--0.24 Å20.34 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.28→25.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 16 179 1570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221504
X-RAY DIFFRACTIONr_bond_other_d0.0020.021336
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9452056
X-RAY DIFFRACTIONr_angle_other_deg0.78833106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77424.56881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4715255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.368159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
X-RAY DIFFRACTIONr_nbd_refined0.2270.2298
X-RAY DIFFRACTIONr_nbd_other0.1920.21413
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2740
X-RAY DIFFRACTIONr_nbtor_other0.0850.2853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.216
X-RAY DIFFRACTIONr_mcbond_it1.8923941
X-RAY DIFFRACTIONr_mcbond_other0.3873373
X-RAY DIFFRACTIONr_mcangle_it2.6951437
X-RAY DIFFRACTIONr_scbond_it4.0588674
X-RAY DIFFRACTIONr_scangle_it5.47911606
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 36 -
Rwork0.293 924 -
obs-960 27.68 %
Refinement TLS params.Method: refined / Origin x: 18.079 Å / Origin y: 26.729 Å / Origin z: 12.492 Å
111213212223313233
T-0.0195 Å20.0085 Å20.0022 Å2--0.0234 Å2-0.0177 Å2--0.0064 Å2
L1.2475 °20.1855 °2-0.1538 °2-1.0151 °2-0.3522 °2--0.5476 °2
S-0.0211 Å °0.0049 Å °-0.096 Å °0.0207 Å °0.0029 Å °-0.0776 Å °0.0201 Å °-0.0252 Å °0.0182 Å °
Refinement TLS groupSelection: ALL

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