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- PDB-1whz: Crystal structure of a hypothetical protein from thermus thermoph... -

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Basic information

Entry
Database: PDB / ID: 1whz
TitleCrystal structure of a hypothetical protein from thermus thermophilus HB8
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha and beta protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


endonuclease activity / mRNA binding
Similarity search - Function
Hypothetical protein. / HicA mRNA interferase family / HicA superfamily / HicA toxin of bacterial toxin-antitoxin, / Metal Transport, Frataxin; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.52 Å
AuthorsKanagawa, M. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein from thermus thermophilus HB8
Authors: Kanagawa, M. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2016Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3582
Polymers8,3221
Non-polymers351
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.040, 27.910, 36.990
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein


Mass: 8322.239 Da / Num. of mol.: 1
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: Q5SH17
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.68 Å3/Da / Density % sol: 26.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.2
Details: PegMME, natrium chloride, Bicine, pH 9.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9000, 0.979105, 0.979416
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 13, 2004
RadiationMonochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.9791051
30.9794161
ReflectionResolution: 1.52→36.99 Å / Num. all: 8647 / % possible obs: 99.6 % / Biso Wilson estimate: 12.8 Å2
Reflection shellResolution: 1.52→1.62 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.52→36.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 482173.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 922 10.7 %RANDOM
Rwork0.148 ---
all0.155 ---
obs0.148 8647 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6231 Å2 / ksol: 0.328647 e/Å3
Displacement parametersBiso mean: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.23 Å2
2---1.48 Å20 Å2
3---1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.52→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms576 0 1 120 697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.035
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d2.2
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 1.52→1.62 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 147 10.3 %
Rwork0.174 1280 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_PROTIN.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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