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- PDB-1wub: Crystal structure of the polyisoprenoid-binding protein, TT1927b,... -

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Basic information

Entry
Database: PDB / ID: 1wub
TitleCrystal structure of the polyisoprenoid-binding protein, TT1927b, from Thermus thermophilus HB8
Componentsconserved hypothetical protein TT1927b
KeywordsLIPID BINDING PROTEIN / beta-barrel / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-OTP / Lipid/polyisoprenoid-binding YceI-like domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHanda, N. / Idaka, M. / Terada, T. / Hamana, H. / Ishizuka, Y. / Park, S.-Y. / Tame, J.R.H. / Doi-Katayama, Y. / Hirota, H. / Kuramitsu, S. ...Handa, N. / Idaka, M. / Terada, T. / Hamana, H. / Ishizuka, Y. / Park, S.-Y. / Tame, J.R.H. / Doi-Katayama, Y. / Hirota, H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8
Authors: Handa, N. / Terada, T. / Doi-Katayama, Y. / Hirota, H. / Tame, J.R. / Park, S.-Y. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 3, 2004Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 21, 2004ID: 1UF6
Revision 1.0Dec 21, 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 / 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: conserved hypothetical protein TT1927b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2212
Polymers19,4981
Non-polymers7231
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.561, 96.948, 109.140
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 conserved hypothetical protein TT1927b / polyisoprenoid-binding protein TT1927b


Mass: 19497.998 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): BL21(DE3)pLysS / References: UniProt: P83815
#2: Chemical ChemComp-OTP / (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE / OCTAPRENYL PYROPHOSPHATE


Mass: 722.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H68O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.21 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.6M Ammonium Sulfate, 5% Dioxane, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 21643 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.034 / Net I/σ(I): 43.8
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.23 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.337 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26272 1009 4.9 %RANDOM
Rwork0.21867 ---
obs0.22078 19738 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: 23.994 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 49 102 1509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211433
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9781944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985175
X-RAY DIFFRACTIONr_chiral_restr0.1360.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021096
X-RAY DIFFRACTIONr_nbd_refined0.2280.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.25
X-RAY DIFFRACTIONr_mcbond_it1.1261.5876
X-RAY DIFFRACTIONr_mcangle_it2.09921414
X-RAY DIFFRACTIONr_scbond_it3.1043557
X-RAY DIFFRACTIONr_scangle_it5.1744.5530
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 59
Rwork0.248 1219

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