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- PDB-2yyb: Crystal structure of TTHA1606 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2yyb
TitleCrystal structure of TTHA1606 from Thermus thermophilus HB8
ComponentsHypothetical protein TTHA1606
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus thermophilus / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / NIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GTP cyclohydrolase 1 type 2 homolog
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTomoike, F. / Nakagwa, N. / Ebihara, A. / Yokoyama, S. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of the conserved hypothetical protein TTHA1606 from Thermus thermophilus HB8.
Authors: Tomoike, F. / Wakamatsu, T. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionApr 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 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: Hypothetical protein TTHA1606
B: Hypothetical protein TTHA1606


Theoretical massNumber of molelcules
Total (without water)53,7332
Polymers53,7332
Non-polymers00
Water36020
1
A: Hypothetical protein TTHA1606
B: Hypothetical protein TTHA1606

A: Hypothetical protein TTHA1606
B: Hypothetical protein TTHA1606

A: Hypothetical protein TTHA1606
B: Hypothetical protein TTHA1606


Theoretical massNumber of molelcules
Total (without water)161,2006
Polymers161,2006
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11030 Å2
ΔGint-61 kcal/mol
Surface area55300 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-6 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.186, 148.186, 196.395
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hypothetical protein TTHA1606


Mass: 26866.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ttha1606 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHX4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 28v/w PEG 400, 0.2M CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 11, 2007
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→42.78 Å / Num. all: 25740 / Num. obs: 25740 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 53.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6.03 / Num. unique all: 2556 / % possible all: 92.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NMP

1nmp


Resolution: 2.6→42.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 143672.6 / 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
Rfree0.283 2463 9.9 %random
Rwork0.239 ---
all-25005 --
obs-25005 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1198 Å2 / ksol: 0.364834 e/Å3
Displacement parametersBiso mean: 42.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å25.16 Å20 Å2
2---2.66 Å20 Å2
3---5.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 0 20 3826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
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: 2.6→2.76 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.386 355 -
Rwork0.318 --
obs-3584 92.6 %

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