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- PDB-1wdj: Crystal structure of TT1808 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1wdj
TitleCrystal structure of TT1808 from Thermus thermophilus HB8
Componentshypothetical protein TT1808
KeywordsStructural genomics / unknown function / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologytt1808, chain A / Putative restriction endonuclease / Nuclease, putative, TT1808 / Putative restriction endonuclease / tt1808, chain A / Restriction endonuclease type II-like / Alpha-Beta Complex / Alpha Beta / Putative restriction endonuclease domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsIdaka, M. / Wada, T. / Murayama, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal Structure Of TT1808 From Thermus Thermophilus HB8
Authors: Idaka, M. / Wada, T. / Murayama, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 17, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: 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 TT1808
B: hypothetical protein TT1808
C: hypothetical protein TT1808


Theoretical massNumber of molelcules
Total (without water)62,4143
Polymers62,4143
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.682, 95.172, 99.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein TT1808


Mass: 20804.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SI60
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 7.5 / Details: MPD, EtOH, pH 7.5, SMALL TUBES, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9790, 0.9793, 0.9760, 0.9830
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 7, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.9761
40.9831
ReflectionResolution: 2→30 Å / Num. obs: 34418 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 16.7 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 86.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20.04 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1277531.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3426 10 %RANDOM
Rwork0.189 ---
obs0.189 34391 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.3311 Å2 / ksol: 0.339699 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---0.94 Å20 Å2
3---2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→20.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 0 255 4363
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.961.5
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scbond_it3.152
X-RAY DIFFRACTIONc_scangle_it4.232.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 485 9.7 %
Rwork0.248 4522 -
obs--83.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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