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- PDB-1uan: Crystal structure of the conserved protein TT1542 from Thermus th... -

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Basic information

Entry
Database: PDB / ID: 1uan
TitleCrystal structure of the conserved protein TT1542 from Thermus thermophilus HB8
Componentshypothetical protein TT1542
Keywordsstructural genomics / unknown function / Rossmann-like / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


bacillithiol biosynthetic process / deacetylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Similarity search - Function
Bacillithiol biosynthesis deacetylase, BshB1 / LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacillithiol biosynthesis deacetylase BshB1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHanda, N. / Terada, T. / Tame, J.R.H. / Park, S.-Y. / Kinoshita, K. / Ota, M. / Nakamura, H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: PROTEIN SCI. / Year: 2003
Title: Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8
Authors: Handa, N. / Terada, T. / Kamewari, Y. / Hamana, H. / Tame, J.R.H. / Park, S.-Y. / Kinoshita, K. / Ota, M. / Nakamura, H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMar 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 TT1542
B: hypothetical protein TT1542


Theoretical massNumber of molelcules
Total (without water)49,6412
Polymers49,6412
Non-polymers00
Water2,810156
1
A: hypothetical protein TT1542
B: hypothetical protein TT1542

A: hypothetical protein TT1542
B: hypothetical protein TT1542

A: hypothetical protein TT1542
B: hypothetical protein TT1542


Theoretical massNumber of molelcules
Total (without water)148,9226
Polymers148,9226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area19600 Å2
ΔGint-114 kcal/mol
Surface area47950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.134, 107.134, 98.617
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein hypothetical protein TT1542 / conserved protein TT1542


Mass: 24820.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q84BR2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammonium sulfate, sodium chloride, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
3100 mMHEPES-HCl1reservoirpH7.1
4100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9821, 0.9808, 0.9803, 0.9752
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98211
20.98081
30.98031
40.97521
ReflectionResolution: 2→20 Å / Num. all: 419509 / Num. obs: 419321 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 9.4 % / Rsym value: 0.034
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.223 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 44178 / % possible obs: 99.3 % / Num. measured all: 406551 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.522 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24258 2245 5 %RANDOM
Rwork0.20085 ---
obs0.20296 42222 100 %-
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: 35.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 0 156 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213499
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9754744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1480.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21551
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2241.52189
X-RAY DIFFRACTIONr_mcangle_it2.25423485
X-RAY DIFFRACTIONr_scbond_it3.5131310
X-RAY DIFFRACTIONr_scangle_it5.9194.51259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 166
Rwork0.247 3071
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8

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