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- PDB-3ld2: The Crystal Structure of smu.2055 from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3ld2
TitleThe Crystal Structure of smu.2055 from Streptococcus mutans UA159
ComponentsPutative acetyltransferase
KeywordsTRANSFERASE / putative acetyltransferase
Function / homology
Function and homology information


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
COENZYME A / Acetyltransferase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSu, X.-D. / Zhan, X.R. / Gao, X.Z. / Liu, X.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of smu.2055 from Streptococcus mutans UA159
Authors: Su, X.-D. / Zhan, X.R. / Gao, X.Z. / Liu, X.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 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 / _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: Putative acetyltransferase
B: Putative acetyltransferase
C: Putative acetyltransferase
D: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9658
Polymers89,8954
Non-polymers3,0704
Water36020
1
A: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2412
Polymers22,4741
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2412
Polymers22,4741
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2412
Polymers22,4741
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2412
Polymers22,4741
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.000, 95.000, 192.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Putative acetyltransferase / smu.2055


Mass: 22473.838 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.2055 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DRZ8
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 0.05M Bis-tris pH 6.5, 0.05M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 29608 / Num. obs: 29430 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.79 Å2
Reflection shellResolution: 2.5→2.6 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.998 Å / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.77 / SU ML: 0.42 / σ(F): 2.04 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2883 2002 6.8 %
Rwork0.2249 27428 -
obs0.2292 29430 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.226 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 86.61 Å2 / Biso mean: 25.128 Å2 / Biso min: 7.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 192 20 5340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015431
X-RAY DIFFRACTIONf_angle_d1.4297373
X-RAY DIFFRACTIONf_dihedral_angle_d24.8672097
X-RAY DIFFRACTIONf_chiral_restr0.085810
X-RAY DIFFRACTIONf_plane_restr0.019920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56240.39351390.29481917X-RAY DIFFRACTION99
2.5624-2.63160.33341440.24771930X-RAY DIFFRACTION100
2.6316-2.70880.3271380.24511946X-RAY DIFFRACTION100
2.7088-2.7960.35831430.24591930X-RAY DIFFRACTION100
2.796-2.89570.31491390.26541928X-RAY DIFFRACTION100
2.8957-3.01130.41751410.28191953X-RAY DIFFRACTION100
3.0113-3.14780.31041420.26211957X-RAY DIFFRACTION100
3.1478-3.31310.29951410.23041943X-RAY DIFFRACTION100
3.3131-3.51960.2941400.21981961X-RAY DIFFRACTION100
3.5196-3.78960.28721480.19181930X-RAY DIFFRACTION100
3.7896-4.16790.21861460.17461991X-RAY DIFFRACTION100
4.1679-4.76390.20371500.14921968X-RAY DIFFRACTION100
4.7639-5.97530.21641460.16032003X-RAY DIFFRACTION100
5.9753-19.99830.2171450.16452071X-RAY DIFFRACTION100

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