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- PDB-2d4p: Crystal structure of TTHA1254 (wild type) from Thermus thermophil... -

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Basic information

Entry
Database: PDB / ID: 2d4p
TitleCrystal structure of TTHA1254 (wild type) from Thermus thermophilus HB8
Componentshypothetical protein TTHA1254
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 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
Similarity search - Function
Protein of unknown function DUF1999 / Protein of unknown function (DUF1999) / 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
N-acetyltransferase domain-containing protein / Fe-S binding reductase, putative
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMizohata, E. / Uchikubo, T. / Kinoshita, Y. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of TTHA1254 (wild type) from Thermus thermophilus HB8
Authors: Mizohata, E. / Uchikubo, T. / Kinoshita, Y. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionOct 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2006Provider: 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 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TTHA1254


Theoretical massNumber of molelcules
Total (without water)15,4851
Polymers15,4851
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein TTHA1254

A: hypothetical protein TTHA1254


Theoretical massNumber of molelcules
Total (without water)30,9692
Polymers30,9692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4120 Å2
ΔGint-24 kcal/mol
Surface area12740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.721, 61.721, 74.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein hypothetical protein TTHA1254


Mass: 15484.720 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72J89, UniProt: Q5SIW0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG3350, Tris, NaCl, Ammonium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 18129

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D4O

2d4o


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.945 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19485 933 5.1 %RANDOM
Rwork0.1683 ---
obs0.16958 17189 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 0 157 1168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211028
X-RAY DIFFRACTIONr_bond_other_d0.0020.02996
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.981386
X-RAY DIFFRACTIONr_angle_other_deg0.82232284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021153
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02232
X-RAY DIFFRACTIONr_nbd_refined0.2070.2157
X-RAY DIFFRACTIONr_nbd_other0.2540.21095
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0490.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3960.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.5642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56621017
X-RAY DIFFRACTIONr_scbond_it2.5433386
X-RAY DIFFRACTIONr_scangle_it4.3294.5369
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
Rfree0.269 67
Rwork0.236 1165
Refinement TLS params.Method: refined / Origin x: 16.2813 Å / Origin y: 21.8618 Å / Origin z: 25.2623 Å
111213212223313233
T0.0052 Å20.0019 Å2-0.0034 Å2-0.0419 Å2-0.0074 Å2--0.025 Å2
L1.571 °2-0.4753 °2-0.73 °2-0.7745 °20.142 °2--1.0355 °2
S0.0523 Å °0.2556 Å °-0.0863 Å °-0.0819 Å °-0.0809 Å °-0.0018 Å °0.0448 Å °-0.1189 Å °0.0286 Å °

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