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- PDB-2zxv: Crystal structure of putative acetyltransferase from T. thermophi... -

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Basic information

Entry
Database: PDB / ID: 2zxv
TitleCrystal structure of putative acetyltransferase from T. thermophilus HB8
ComponentsPutative uncharacterized protein TTHA1799
KeywordsTRANSFERASE / alpha/beta protein / IY-substitution / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / identical protein binding
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
N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionJan 8, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Putative uncharacterized protein TTHA1799
B: Putative uncharacterized protein TTHA1799
C: Putative uncharacterized protein TTHA1799
D: Putative uncharacterized protein TTHA1799


Theoretical massNumber of molelcules
Total (without water)89,1544
Polymers89,1544
Non-polymers00
Water3,171176
1
A: Putative uncharacterized protein TTHA1799
C: Putative uncharacterized protein TTHA1799


Theoretical massNumber of molelcules
Total (without water)44,5772
Polymers44,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein TTHA1799
D: Putative uncharacterized protein TTHA1799


Theoretical massNumber of molelcules
Total (without water)44,5772
Polymers44,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative uncharacterized protein TTHA1799


Theoretical massNumber of molelcules
Total (without water)22,2881
Polymers22,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Putative uncharacterized protein TTHA1799


Theoretical massNumber of molelcules
Total (without water)22,2881
Polymers22,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Putative uncharacterized protein TTHA1799


Theoretical massNumber of molelcules
Total (without water)22,2881
Polymers22,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Putative uncharacterized protein TTHA1799


Theoretical massNumber of molelcules
Total (without water)22,2881
Polymers22,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.8, 127.8, 122.1
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Putative uncharacterized protein TTHA1799 / RimL


Mass: 22288.467 Da / Num. of mol.: 4 / Mutation: Y35(IYR)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1799 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SHD1, ribosomal-protein-alanine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2M MgCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42723 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 14.5 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.089 / Net I/σ(I): 28.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.296 / % possible all: 82.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pdb entry 2Z10

2z10


Resolution: 2.3→30.13 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2686186.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED DATA. THE TWINNING OPERATOR IS (H,K,L) -> (h, -k, -l) AND THE TWINNING FRACTION is 0.443
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4022 9.4 %RANDOM
Rwork0.228 ---
obs-42627 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.3764 Å2 / ksol: 0.323298 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.53 Å20 Å20 Å2
2--4.53 Å20 Å2
3----9.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6140 0 0 176 6316
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.57
X-RAY DIFFRACTIONc_mcbond_it3.051.5
X-RAY DIFFRACTIONc_mcangle_it4.762
X-RAY DIFFRACTIONc_scbond_it4.622
X-RAY DIFFRACTIONc_scangle_it6.492.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 574 9.1 %
Rwork0.402 5715 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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