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- PDB-1j3m: Crystal structure of the conserved hypothetical protein TT1751 fr... -

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Basic information

Entry
Database: PDB / ID: 1j3m
TitleCrystal structure of the conserved hypothetical protein TT1751 from Thermus thermophilus HB8
Componentsthe conserved hypothetical protein TT1751
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


TT1751-like domain / Uncharacterised conserved protein UCP021774 / Domain of unknown function DUF302 / TT1751-like domain superfamily / Domain of unknown function DUF302 / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SULFITE ION / DUF302 domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKishishita, S. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Park, S.-Y. / Tame, R.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8
Authors: Kishishita, S. / Tatsuguchi, A. / Ushikoshi-Nakayama, R. / Terada, T. / Kuramitsu, S. / Park, S.-Y. / Tame, J.R. / Shirouzu, M. / Yokoyama, S.
History
DepositionFeb 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: the conserved hypothetical protein TT1751
B: the conserved hypothetical protein TT1751
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0273
Polymers27,9472
Non-polymers801
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-25 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.603, 78.811, 44.688
Angle α, β, γ (deg.)90.00, 116.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein the conserved hypothetical protein TT1751


Mass: 13973.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q84BQ8
#2: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: microbatch crystallization / pH: 5.6
Details: PEGMME 5000, Ammonium Sulfate, pH 5.6, Microbatch Crystallization, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9804, 0.9808, 0.9825, 0.9720
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2002 / Details: monochromator
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98041
20.98081
30.98251
40.9721
ReflectionResolution: 2→50 Å / Num. obs: 16980 / % possible obs: 97.9 % / Observed criterion σ(I): 70405 / Redundancy: 4.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.138 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.188 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25884 819 4.9 %RANDOM
Rwork0.19365 ---
obs0.19694 15778 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: 29.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å21.97 Å2
2---0.56 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 4 112 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.152.0272633
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1710.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2839
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.271.51272
X-RAY DIFFRACTIONr_mcangle_it2.24722030
X-RAY DIFFRACTIONr_scbond_it3.83675
X-RAY DIFFRACTIONr_scangle_it6.124.5603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 46
Rwork0.225 880

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