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- PDB-3g8w: Crystal structure of a probable acetyltransferase from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 3g8w
TitleCrystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228
ComponentsLactococcal prophage ps3 protein 05
KeywordsTRANSFERASE / APC61042 / acetyltransferase / Staphylococcus epidermidis ATCC 12228 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
CITRATE ANION / Lactococcal prophage ps3 protein 05 / Lactococcal prophage ps3 protein 05
Similarity search - Component
Biological speciesStaphylococcus epidermidis ATCC 12228 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsTan, K. / Sather, A. / Marshall, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228.
Authors: Tan, K. / Sather, A. / Marshall, N. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 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: Lactococcal prophage ps3 protein 05
B: Lactococcal prophage ps3 protein 05
C: Lactococcal prophage ps3 protein 05
D: Lactococcal prophage ps3 protein 05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,57917
Polymers79,9024
Non-polymers2,67713
Water37821
1
A: Lactococcal prophage ps3 protein 05
B: Lactococcal prophage ps3 protein 05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1958
Polymers39,9512
Non-polymers1,2446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-3.8 kcal/mol
Surface area16820 Å2
MethodPISA
2
C: Lactococcal prophage ps3 protein 05
D: Lactococcal prophage ps3 protein 05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3849
Polymers39,9512
Non-polymers1,4337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-2.3 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.960, 110.409, 220.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN. IT IS LIKELY A DIMER WITH THE ASSEMBLY SHOWN IN REMARK 350.

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Components

#1: Protein
Lactococcal prophage ps3 protein 05


Mass: 19975.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis ATCC 12228 (bacteria)
Gene: SE_0588 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8CPX3, UniProt: A0A0H2VFJ4*PLUS
#2: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.69 Å3/Da / Density % sol: 66.69 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1M CHES, 1.0M Sodium citrate, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97940
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2008 / Details: mirror
RadiationMonochromator: Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.97941
ReflectionResolution: 2.7→50 Å / Num. all: 32550 / Num. obs: 32550 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 37.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1598 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→49.39 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 23.19 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.46 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Monomer D is partially disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.25626 1639 5.1 %RANDOM
Rwork0.21323 ---
all0.21542 30770 --
obs0.21542 30770 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5257 0 169 21 5447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9427501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.56225.638298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.56215907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4961515
X-RAY DIFFRACTIONr_chiral_restr0.120.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024150
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.07823247
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8935210
X-RAY DIFFRACTIONr_scbond_it1.18422293
X-RAY DIFFRACTIONr_scangle_it1.79332291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 117 -
Rwork0.244 2140 -
obs-2257 94.99 %
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)
13.99860.4803-0.38753.8671-0.90245.55590.167-0.0030.32440.0797-0.075-0.2076-0.42840.6037-0.0920.0833-0.1019-0.00670.13710.01430.293314.04166.91271.408
22.07931.41840.05394.43980.08588.2980.0658-0.6248-0.10.4891-0.273-0.5517-0.28631.16840.20730.3935-0.2134-0.01140.46630.04150.337713.8167.40699.586
34.5202-2.4564-1.30516.11341.91075.19380.52660.4723-0.5396-0.3415-0.72560.22130.31320.11170.1990.20810.2159-0.07150.2708-0.09610.42158.60439.15750.229
41.37960.34061.08333.38492.12646.87990.63421.346-0.1637-1.4468-0.7909-0.0503-0.21840.05550.15671.42051.2548-0.2361.9412-0.37830.72787.76738.76121.869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 162
2X-RAY DIFFRACTION2B2 - 165
3X-RAY DIFFRACTION3C1 - 162
4X-RAY DIFFRACTION4D2 - 162

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