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- PDB-2plg: Crystal structure of T110839 protein from Synechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 2plg
TitleCrystal structure of T110839 protein from Synechococcus elongatus
ComponentsTll0839 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical / uncharacterized / DUF1821 / 10450c / NYSGXRC / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyPutative sensory transduction regulator YbjN / Putative bacterial sensory transduction regulator / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta / Tll0839 protein
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMadegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of T110839 protein from Synechococcus elongatus.
Authors: Madegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Tll0839 protein
B: Tll0839 protein


Theoretical massNumber of molelcules
Total (without water)36,1122
Polymers36,1122
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-20 kcal/mol
Surface area14160 Å2
MethodPISA
2
A: Tll0839 protein

A: Tll0839 protein

B: Tll0839 protein

B: Tll0839 protein


Theoretical massNumber of molelcules
Total (without water)72,2234
Polymers72,2234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/41
Buried area7260 Å2
ΔGint-45 kcal/mol
Surface area26310 Å2
MethodPISA
3
A: Tll0839 protein
B: Tll0839 protein

A: Tll0839 protein
B: Tll0839 protein


Theoretical massNumber of molelcules
Total (without water)72,2234
Polymers72,2234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8030 Å2
ΔGint-57 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.185, 98.185, 144.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Tll0839 protein


Mass: 18055.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: BP-1 / Gene: tll0839 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DKM0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 4.83 Å3/Da / Density % sol: 74.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.0 M Lithium sulfate, 0.5 M Ammonium sulfate, 0.1 M Tri-Na citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2007 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. all: 26434 / Num. obs: 26434 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.6 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.63 / Num. unique all: 2558 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→37.54 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 93266.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled ...Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines. Data beyond 2.6 A were not used in the refinement since the quality of the data was poor.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1059 4.8 %RANDOM
Rwork0.216 ---
obs0.216 21891 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3367 Å2 / ksol: 0.385523 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.75 Å20 Å20 Å2
2---5.75 Å20 Å2
3---11.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 0 106 2416
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 166 4.9 %
Rwork0.28 3238 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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