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- PDB-2z10: Crystal structure of putative acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 2z10
TitleCrystal structure of putative acetyltransferase
ComponentsRibosomal-protein-alanine acetyltransferase
KeywordsTRANSFERASE / alpha/beta protein / Acyltransferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ribosomal-protein-alanine N-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal-protein-alanine acetyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.77 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2009
Title: Genetic Encoding of 3-Iodo-l-Tyrosine in Escherichia coli for Single-Wavelength Anomalous Dispersion Phasing in Protein Crystallography
Authors: Sakamoto, K. / Murayama, K. / Oki, K. / Iraha, F. / Kato-Murayama, M. / Takahashi, M. / Ohtake, K. / Kobayashi, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal-protein-alanine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)22,2881
Polymers22,2881
Non-polymers00
Water3,315184
1
A: Ribosomal-protein-alanine acetyltransferase

A: Ribosomal-protein-alanine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)44,5772
Polymers44,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2030 Å2
ΔGint-0 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.401, 71.401, 99.255
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribosomal-protein-alanine acetyltransferase


Mass: 22288.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q72HN8, ribosomal-protein-alanine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15M ammonium acetate, 0.1M bis-tris pH5.5, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 28933 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.042 / Net I/σ(I): 34.3
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 8.9 / Rsym value: 0.266 / % possible all: 90.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→30.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1264710.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1413 4.9 %RANDOM
Rwork0.206 ---
obs-28876 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.5752 Å2 / ksol: 0.348736 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-4.31 Å20.75 Å20 Å2
2--4.31 Å20 Å2
3----8.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.77→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 184 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 1.77→1.88 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 229 5 %
Rwork0.266 4390 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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