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- PDB-2aj6: Crystal structure of a putative gnat family acetyltransferase (mw... -

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Basic information

Entry
Database: PDB / ID: 2aj6
TitleCrystal structure of a putative gnat family acetyltransferase (mw0638) from staphylococcus aureus subsp. aureus at 1.63 A resolution
Componentshypothetical protein MW0638
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / 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
Similarity search - Domain/homology
Unknown ligand / N-acetyltransferase domain-containing protein / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein MW0638 from Staphylococcus aureus MW2 at 1.63 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein MW0638
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2323
Polymers19,1361
Non-polymers962
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.058, 74.856, 90.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

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Components

#1: Protein hypothetical protein MW0638


Mass: 19136.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: np_645455.1 / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8NXQ8, UniProt: A0A0H3JUY4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.9
Details: 0.2M MgSO4, 20.0% PEG-3350, No Buffer, pH 5.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979341
ReflectionResolution: 1.5→28.87 Å / Num. obs: 17165 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.63-1.6787.72.50.5511.410980.551
1.67-1.72942.90.4651.611470.465
1.72-1.7799.73.50.3542.212040.354
1.77-1.821003.70.312.411800.31
1.82-1.881003.60.2233.411370.223
1.88-1.951003.60.1634.410930.163
1.95-2.021003.60.1225.810630.122
2.02-2.11003.70.16.910260.1
2.1-2.21003.60.0818.89770.081
2.2-2.311003.60.0788.59540.078
2.31-2.431003.60.079.68910.07
2.43-2.581003.60.05911.48600.059
2.58-2.761003.60.05611.48000.056
2.76-2.981003.60.05611.17570.056
2.98-3.261003.60.05411.37120.054
3.26-3.641003.60.03915.16280.039
3.64-4.2199.93.50.038165590.038
4.21-5.1599.53.50.03716.74770.037
5.15-7.2999.43.40.04114.13800.041
7.29-28.8796.43.10.0624.62220.062

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.63→28.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.553 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.096
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.NO DENSITY OBSERVED FOR RESIDUES 119-147. 3.EXTRA DENSITY OBSERVED BETWEEN RESIDUES 87-92 HAS BEEN MODELED UNKNOWN LIGAND. HOMOLOGY ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.NO DENSITY OBSERVED FOR RESIDUES 119-147. 3.EXTRA DENSITY OBSERVED BETWEEN RESIDUES 87-92 HAS BEEN MODELED UNKNOWN LIGAND. HOMOLOGY SEARCHES INDICATE THAT THIS IS A PUTA COENZYME-A BINDING SITE. 4.ONE SULPHATE GROUP WAS FOUND IN THE MODEL DURING THE REFINEMEN FROMTHE CRYSTALLIZATION CONDITION WITH MGSO4.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 830 4.8 %RANDOM
Rwork0.181 ---
all0.183 ---
obs-16334 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.222 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2--0.06 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.63→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 15 122 1117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221047
X-RAY DIFFRACTIONr_bond_other_d0.0010.02928
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9311423
X-RAY DIFFRACTIONr_angle_other_deg1.21532170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3835130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.89624.61552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47215198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.146155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02210
X-RAY DIFFRACTIONr_nbd_refined0.3040.2236
X-RAY DIFFRACTIONr_nbd_other0.1850.2960
X-RAY DIFFRACTIONr_nbtor_refined0.180.2513
X-RAY DIFFRACTIONr_nbtor_other0.0850.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.213
X-RAY DIFFRACTIONr_mcbond_it2.1423649
X-RAY DIFFRACTIONr_mcbond_other0.513253
X-RAY DIFFRACTIONr_mcangle_it2.90951015
X-RAY DIFFRACTIONr_scbond_it5.5138465
X-RAY DIFFRACTIONr_scangle_it7.26111404
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 61 -
Rwork0.289 1034 -
obs--87.04 %
Refinement TLS params.Method: refined / Origin x: 4.6567 Å / Origin y: 14.3597 Å / Origin z: 13.9026 Å
111213212223313233
T-0.1576 Å20.0118 Å2-0.0151 Å2--0.1367 Å2-0.0245 Å2---0.1562 Å2
L0.9834 °20.18 °20.63 °2-2.1993 °2-1.2433 °2--3.5469 °2
S0.0458 Å °-0.0647 Å °-0.0372 Å °-0.1223 Å °-0.0102 Å °0.0537 Å °0.0233 Å °-0.0237 Å °-0.0356 Å °

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