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- PDB-1ufa: Crystal structure of TT1467 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1ufa
TitleCrystal structure of TT1467 from Thermus thermophilus HB8
ComponentsTT1467 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


alpha-glucan biosynthetic process / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process
Similarity search - Function
: / 1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain ...: / 1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan branching enzyme TTHA1902 / 1,4-alpha-glucan branching enzyme TTHA1902
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsIdaka, M. / Terada, T. / Murayama, K. / Yamaguchi, H. / Nureki, O. / Ishitani, R. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal structure of TT1467 from Thermus thermophilus HB8
Authors: Idaka, M. / Terada, T. / Murayama, K. / Yamaguchi, H. / Nureki, O. / Ishitani, R. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TT1467 protein


Theoretical massNumber of molelcules
Total (without water)59,6271
Polymers59,6271
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.376, 119.376, 73.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein TT1467 protein


Mass: 59626.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: P84162, UniProt: Q5SH28*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 44.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Lithium Sulfate, Sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 29307 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 26.4 Å2
Reflection shellResolution: 2.15→2.23 Å / % possible all: 89.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
autoSHARPphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2401211.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2753 10 %RANDOM
Rwork0.187 ---
obs0.187 27591 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7439 Å2 / ksol: 0.361851 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 0 296 4412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 457 10.2 %
Rwork0.281 4035 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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