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- PDB-1ufo: Crystal Structure of TT1662 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1ufo
TitleCrystal Structure of TT1662 from Thermus thermophilus
Componentshypothetical protein TT1662
KeywordsHYDROLASE / alpha-beta fold / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / membrane / Alpha Beta / Hydrolase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsMurayama, K. / Shirouzu, M. / Terada, T. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of TT1662 from Thermus thermophilus HB8: a member of the alpha/beta hydrolase fold enzymes.
Authors: Murayama, K. / Shirouzu, M. / Terada, T. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJun 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TT1662
B: hypothetical protein TT1662
C: hypothetical protein TT1662
D: hypothetical protein TT1662
E: hypothetical protein TT1662
F: hypothetical protein TT1662


Theoretical massNumber of molelcules
Total (without water)157,5416
Polymers157,5416
Non-polymers00
Water33,0581835
1
A: hypothetical protein TT1662
B: hypothetical protein TT1662


Theoretical massNumber of molelcules
Total (without water)52,5142
Polymers52,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: hypothetical protein TT1662
D: hypothetical protein TT1662


Theoretical massNumber of molelcules
Total (without water)52,5142
Polymers52,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: hypothetical protein TT1662
F: hypothetical protein TT1662


Theoretical massNumber of molelcules
Total (without water)52,5142
Polymers52,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.857, 129.857, 70.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
hypothetical protein TT1662


Mass: 26256.873 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P83821
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1835 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% PEG3350, 0.2M KF, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG33501reservoir
20.2 Mpotassium fluoride1reservoir
34.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 174213 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.072
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.321 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 1336033 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.321

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→21.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2514544.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 17296 9.9 %RANDOM
Rwork0.1699 ---
obs-174137 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.0509 Å2 / ksol: 0.465362 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å21.13 Å20 Å2
2--1.6 Å20 Å2
3----3.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11153 0 0 1835 12988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 2853 9.9 %
Rwork0.2 26064 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.49

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