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- PDB-1z9u: Structural Genomics, The crystal structure of the acetyl transfer... -

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Basic information

Entry
Database: PDB / ID: 1z9u
TitleStructural Genomics, The crystal structure of the acetyl transferase, modifies N-terminal serine of 50S ribosomal subunit protein L7/L12 from Salmonella typhimurium
Componentsacetyl transferase
KeywordsTRANSFERASE / acetyl transferase / L7/L12 / Salmonella typhimurium / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl 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
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of the acetyl transferase, modifies N-terminal serine of 50S ribosomal subunit protein L7/L12 from Salmonella typhimurium
Authors: Zhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionApr 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: acetyl transferase
B: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,02910
Polymers41,2612
Non-polymers7698
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: acetyl transferase
hetero molecules

B: acetyl transferase
hetero molecules

A: acetyl transferase
hetero molecules

A: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,05920
Polymers82,5224
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
crystal symmetry operation6_664x-y+1,x+1,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area8270 Å2
ΔGint-292 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.700, 86.700, 237.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThis protein existed as dimer. MolA and MolB represent the dimer in the assymetric unit.

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Components

#1: Protein acetyl transferase


Mass: 20630.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: GI:16764955 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8ZPC0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.186 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0M Ammonium sulphate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9797, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Feb 5, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 2.2→50 Å / Num. all: 26396 / Num. obs: 26286 / % possible obs: 99.58 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 48.87 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 32.55
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3 / Num. unique all: 2544 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.067 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25673 1394 5 %RANDOM
Rwork0.21706 ---
all0.21903 26396 --
obs0.21903 26286 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 40 249 3102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212901
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9433922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01924.013152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68215503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8261522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022198
X-RAY DIFFRACTIONr_nbd_refined0.2050.21292
X-RAY DIFFRACTIONr_nbtor_refined0.30.21912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.226
X-RAY DIFFRACTIONr_mcbond_it0.6371.51805
X-RAY DIFFRACTIONr_mcangle_it1.01722764
X-RAY DIFFRACTIONr_scbond_it1.52931280
X-RAY DIFFRACTIONr_scangle_it2.2934.51158
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 110 -
Rwork0.277 1827 -
obs--97.39 %
Refinement TLS params.Method: refined / Origin x: -15.845 Å / Origin y: 49.729 Å / Origin z: 6.516 Å
111213212223313233
T-0.1758 Å2-0.0086 Å20.0347 Å2--0.0809 Å2-0.0258 Å2---0.269 Å2
L2.9185 °21.2028 °2-0.9229 °2-1.0209 °2-0.3241 °2--1.4219 °2
S0.2405 Å °-0.1579 Å °0.2773 Å °0.1472 Å °-0.1151 Å °0.1256 Å °-0.2712 Å °0.0394 Å °-0.1254 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 403 - 40
2X-RAY DIFFRACTION1AA43 - 10043 - 100
3X-RAY DIFFRACTION1AA101 - 175101 - 175
4X-RAY DIFFRACTION1BB2 - 402 - 40
5X-RAY DIFFRACTION1BB41 - 10041 - 100
6X-RAY DIFFRACTION1BB101 - 175101 - 175

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