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- PDB-2fck: Structure of a putative ribosomal-protein-serine acetyltransferas... -

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Basic information

Entry
Database: PDB / ID: 2fck
TitleStructure of a putative ribosomal-protein-serine acetyltransferase from Vibrio cholerae.
Componentsribosomal-protein-serine acetyltransferase, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Vibrio cholerae / serine acetyltransferase / ribosomal-protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peptide-alanine-alpha-N-acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / cytoplasm
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
NITRATE ION / Ribosomal-protein-serine acetyltransferase / Ribosomal-protein-serine acetyltransferase, putative
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCuff, M.E. / Li, H. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of an acetyltransferase protein from Vibrio cholerae strain N16961.
Authors: Cuff, M.E. / Li, H. / Moy, S. / Watson, J. / Cipriani, A. / Joachimiak, A.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 16, 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
Remark 300 BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ... BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribosomal-protein-serine acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,77614
Polymers20,9401
Non-polymers83613
Water4,288238
1
A: ribosomal-protein-serine acetyltransferase, putative
hetero molecules

A: ribosomal-protein-serine acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,55328
Polymers41,8812
Non-polymers1,67226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)53.051, 103.065, 37.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ribosomal-protein-serine acetyltransferase, putative


Mass: 20940.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Species: Vibrio cholerae / Strain: N16961 / Gene: VC1889 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KQV9, UniProt: A0A0H3AIE8*PLUS
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane, 4M NaNO3, sucrose, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915, 0.97929
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979291
ReflectionResolution: 1.7→50 Å / Num. all: 22626 / Num. obs: 22626 / % possible obs: 95.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.744 Å / % possible all: 86.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
PHENIXphasing
autoSHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.916 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24394 1156 5.1 %RANDOM
Rwork0.21075 ---
obs0.21239 21470 95.84 %-
all-22626 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.938 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 54 238 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221575
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.962132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12224.28684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63215258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7521512
X-RAY DIFFRACTIONr_chiral_restr0.120.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021269
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.2795
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21052
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3890.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3450.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.5988
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76621486
X-RAY DIFFRACTIONr_scbond_it2.83682
X-RAY DIFFRACTIONr_scangle_it3.9474.5646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 74 -
Rwork0.272 1419 -
obs--86.3 %
Refinement TLS params.Method: refined / Origin x: 33.632 Å / Origin y: 36.457 Å / Origin z: 21.151 Å
111213212223313233
T-0.1709 Å2-0.0066 Å20.0065 Å2--0.381 Å2-0.0377 Å2---0.4017 Å2
L1.3431 °20.051 °2-0.1812 °2-3.6172 °2-1.2939 °2--0.8737 °2
S0.0637 Å °-0.1611 Å °-0.005 Å °0.1541 Å °0.038 Å °-0.1157 Å °0.0122 Å °0.1344 Å °-0.1017 Å °

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