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- PDB-2d4o: Crystal structure of TTHA1254 (I68M mutant) from Thermus thermoph... -

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Basic information

Entry
Database: PDB / ID: 2d4o
TitleCrystal structure of TTHA1254 (I68M mutant) from Thermus thermophilus HB8
Componentshypothetical protein TTHA1254Hypothesis
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
Fe-S binding reductase, putative
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 (I68M mutant) 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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

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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)15,6431
Polymers15,6431
Non-polymers00
Water1,74797
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)31,2872
Polymers31,2872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4210 Å2
ΔGint-24 kcal/mol
Surface area12900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.463, 58.463, 77.679
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 / Hypothesis


Mass: 15643.442 Da / Num. of mol.: 1 / Mutation: I68M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q72J89
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, Hepes, NaCl, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96300, 0.97896, 0.97932
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 30, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9631
20.978961
30.979321
ReflectionResolution: 1.8→50 Å / Num. obs: 14538

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.149 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23574 705 5 %RANDOM
Rwork0.18041 ---
obs0.18305 13292 95.14 %-
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: 17.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 0 97 1108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211028
X-RAY DIFFRACTIONr_bond_other_d0.0020.02994
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.981385
X-RAY DIFFRACTIONr_angle_other_deg0.82732280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085129
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_restr0.0830.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021153
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02232
X-RAY DIFFRACTIONr_nbd_refined0.2050.2153
X-RAY DIFFRACTIONr_nbd_other0.2510.21041
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.440.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7641.5642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38921016
X-RAY DIFFRACTIONr_scbond_it2.6193386
X-RAY DIFFRACTIONr_scangle_it4.4064.5369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 53
Rwork0.313 726
Refinement TLS params.Method: refined / Origin x: 14.7499 Å / Origin y: 31.7522 Å / Origin z: 26.6841 Å
111213212223313233
T0.0669 Å20.0016 Å20.0125 Å2-0.0121 Å2-0.0037 Å2--0.042 Å2
L1.3322 °2-0.1006 °20.7346 °2-0.2667 °2-0.1981 °2--0.7501 °2
S0.0267 Å °0.0878 Å °0.0395 Å °-0.0889 Å °-0.0104 Å °-0.0256 Å °0.0342 Å °0.0692 Å °-0.0163 Å °

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