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- PDB-1j27: Crystal structure of a hypothetical protein, TT1725, from Thermus... -

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Basic information

Entry
Database: PDB / ID: 1j27
TitleCrystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7A resolution
Componentshypothetical protein TT1725
Keywordsstructural genomics / unknown function / hypothetical protein from Thermus thermophilus HB8 / MAD / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyTT1725-like / Protein of unknown function DUF503 / TT1725-like superfamily / Protein of unknown function (DUF503) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DUF503 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsSeto, A. / Shirouzu, M. / Terada, T. / Murayama, K. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2003
Title: Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution
Authors: Seto, A. / Shirouzu, M. / Terada, T. / Murayama, K. / Kuramitsu, S. / Yokoyama, S.
History
DepositionDec 26, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / 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 TT1725


Theoretical massNumber of molelcules
Total (without water)11,4211
Polymers11,4211
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein TT1725

A: hypothetical protein TT1725


Theoretical massNumber of molelcules
Total (without water)22,8422
Polymers22,8422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2230 Å2
ΔGint-20 kcal/mol
Surface area9680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.533, 68.388, 58.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein hypothetical protein TT1725


Mass: 11421.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TT1725 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q84BR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.9 mg/mlprotein1drop
210 mMTris1droppH8.5
32.5 %PEG33501drop
475 mMsodium sulfate1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 15362 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.7 Å2
Reflection
*PLUS
Highest resolution: 1.7 Å / % possible obs: 98.7 % / Num. measured all: 71421 / Rmerge(I) obs: 0.028
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 89.6 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 13.8

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→21.48 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1149962.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1439 10.1 %RANDOM
Rwork0.178 ---
all0.178 ---
obs0.178 14178 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.5761 Å2 / ksol: 0.451101 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--1.15 Å20 Å2
3---0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→21.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 0 0 129 907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.2
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2 212 9.1 %
Rwork0.172 2110 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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