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- PDB-4ioh: Crystal Structure of the Tll1086 protein from Thermosynechococcus... -

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Basic information

Entry
Database: PDB / ID: 4ioh
TitleCrystal Structure of the Tll1086 protein from Thermosynechococcus elongatus, Northeast Structural Genomics Consortium Target TeR258
ComponentsTll1086 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF2237 / Protein of unknown function DUF2237 / Uncharacterized protein conserved in bacteria (DUF2237) / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Alpha Beta / Tll1086 protein
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, X. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, X. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Tll1086 protein from Thermosynechococcus elongatus.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, X. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Data collection
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tll1086 protein


Theoretical massNumber of molelcules
Total (without water)14,9081
Polymers14,9081
Non-polymers00
Water30617
1
A: Tll1086 protein

A: Tll1086 protein


Theoretical massNumber of molelcules
Total (without water)29,8172
Polymers29,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2960 Å2
ΔGint-25 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.768, 87.768, 76.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

21A-216-

HOH

Detailsdimer,35.35 kD,91.5%, heptamer,109.8 kD,4.5%

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Components

#1: Protein Tll1086 protein


Mass: 14908.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: tll1086 / Plasmid: TeR258-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8DJY4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 8
Details: 1.11M sodium phosphate, 0.1M Tris-HCl, pH 8.0, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 10991 / Num. obs: 10905 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.5
Reflection shellResolution: 2.53→2.65 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.0127 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1422 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.53→33.999 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.51 / Stereochemistry target values: ML
Details: Cys15 makes a disulfide bond with Cys42 form symmetry-related mate (x,x-y,-z+1/6 + (0 0 0))
RfactorNum. reflection% reflectionSelection details
Rfree0.292 485 4.45 %RANDOM
Rwork0.24 ---
obs0.243 10899 99.45 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.871 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 155.41 Å2 / Biso mean: 91.813 Å2 / Biso min: 39.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.604 Å2-0 Å2-0 Å2
2--1.604 Å20 Å2
3----3.207 Å2
Refinement stepCycle: LAST / Resolution: 2.53→33.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 0 17 919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01928
X-RAY DIFFRACTIONf_angle_d1.3991259
X-RAY DIFFRACTIONf_chiral_restr0.082141
X-RAY DIFFRACTIONf_plane_restr0.006165
X-RAY DIFFRACTIONf_dihedral_angle_d18.884328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5297-2.57110.3581540.3563459361399
2.895-3.6470.3161790.26534873666100
3.647-34.0020.271520.2153468362099

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