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- PDB-4e2a: Crystal Structure of the Putative acetyltransferase from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 4e2a
TitleCrystal Structure of the Putative acetyltransferase from Streptococcus mutans
ComponentsPutative acetyltransferase
KeywordsTRANSFERASE / Alpha Beta / Alpha and Beta Proteins (a+b) / N-acetyltransferase activity
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
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, G.L. / Nie, J.K. / Li, L.F. / Su, X.D.
Citation
Journal: To be Published
Title: Crystal Structure of the Putative acetyltransferase from Streptococcus mutans
Authors: Li, G.L. / Nie, J.K. / Li, L.F. / Su, X.D.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Solid-liquid interface method (SLIM): a new crystallization method for proteins.
Authors: Brostromer, E. / Nan, J. / Li, L.F. / Su, X.D.
#2: Journal: J.Biol.Chem. / Year: 2005
Title: Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase.
Authors: Forouhar, F. / Lee, I.S. / Vujcic, J. / Vujcic, S. / Shen, J. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Porter, C.W. / Tong, L.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetyltransferase
B: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)47,2132
Polymers47,2132
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-10 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.700, 75.700, 80.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 3 - 172 / Label seq-ID: 37 - 206

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN A AND (RESSEQ 3:172)AA
2CHAIN B AND (RESSEQ 3:172)BB

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Components

#1: Protein Putative acetyltransferase


Mass: 23606.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_1511c / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: Q8DT67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 289.2 K / Method: solid-liquid interface method / pH: 7
Details: 0.2M Magnesium formate, 20% PEG 3350, pH 7.0, SOLID-LIQUID INTERFACE METHOD, temperature 289.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 29, 2010
RadiationMonochromator: TOROIDAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30907 / % possible obs: 95.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 18.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.087 / Net I/σ(I): 22.83
Reflection shellResolution: 2→2.1 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 6.21 / Num. unique all: 2192 / Rsym value: 0.485 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TIQ

1tiq


Resolution: 2→18.996 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.809 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1465 4.97 %RANDOM
Rwork0.2148 ---
obs0.2162 29476 95.5 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.887 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 94.08 Å2 / Biso mean: 33.8687 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.6787 Å2-0 Å20 Å2
2---0.6787 Å2-0 Å2
3---1.3575 Å2
Refinement stepCycle: LAST / Resolution: 2→18.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 0 250 3054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092864
X-RAY DIFFRACTIONf_angle_d1.123858
X-RAY DIFFRACTIONf_chiral_restr0.105417
X-RAY DIFFRACTIONf_plane_restr0.003485
X-RAY DIFFRACTIONf_dihedral_angle_d14.0861032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1399X-RAY DIFFRACTIONPOSITIONAL0.037
12B1399X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07140.28821590.243629003059100
2.0714-2.15430.28791340.246129303064100
2.1543-2.25220.39851190.32812348246780
2.2522-2.37070.40521130.34342296240978
2.3707-2.51890.26711720.227729213093100
2.5189-2.71290.2791500.24529043054100
2.7129-2.98490.28411540.23129343088100
2.9849-3.41470.20581650.203629253090100
3.4147-4.29390.17891410.18342879302097
4.2939-18.99710.20381580.170329743132100

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