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- PDB-2cu5: Crystal Structure Of The Conserved Hypothetical Protein TT1486 Fr... -

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Basic information

Entry
Database: PDB / ID: 2cu5
TitleCrystal Structure Of The Conserved Hypothetical Protein TT1486 From Thermus Thermophilus HB8
ComponentsConserved Hypothetical Protein TT1486
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus Thermophilus HB8 / Conserved Hypothetical Protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyYjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / UPF0047 protein YjbQ-like / Jelly Rolls / Sandwich / Mainly Beta / Secondary thiamine-phosphate synthase enzyme
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSatoh, S. / Nakagawa, N. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of The Conserved Hypothetical Protein TT1486 From Thermus Thermophilus HB8
Authors: Satoh, S. / Nakagawa, N. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Conserved Hypothetical Protein TT1486
B: Conserved Hypothetical Protein TT1486
C: Conserved Hypothetical Protein TT1486


Theoretical massNumber of molelcules
Total (without water)43,2953
Polymers43,2953
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-27 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.498, 45.293, 96.523
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Conserved Hypothetical Protein TT1486


Mass: 14431.639 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.85 Å3/Da / Density % sol: 32.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Sodium Chloride, Tris-HCl, Glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→44.82 Å / Num. all: 29020 / Num. obs: 29020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.43 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.1
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 5.48 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2888 / Rsym value: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VMH

1vmh


Resolution: 1.84→41.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1616402.7 / 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
Rfree0.239 1476 5.1 %RANDOM
Rwork0.199 ---
all0.209 29020 --
obs0.199 29019 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3149 Å2 / ksol: 0.374358 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.84→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 0 224 3240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 233 4.9 %
Rwork0.225 4569 -
obs-4731 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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