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- PDB-1pil: STRUCTURE OF THE ESCHERICHIA COLI SIGNAL TRANSDUCING PROTEIN PII -

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Basic information

Entry
Database: PDB / ID: 1pil
TitleSTRUCTURE OF THE ESCHERICHIA COLI SIGNAL TRANSDUCING PROTEIN PII
ComponentsSIGNAL TRANSDUCING PROTEIN P2
KeywordsNITROGEN REGULATORY PROTEIN
Function / homology
Function and homology information


regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / small molecule binding / enzyme regulator activity / enzyme activator activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nitrogen regulatory protein P-II 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsOllis, D.L. / Cheah, U.E. / Carr, P.D. / Suffolk, P.M.
Citation
Journal: Structure / Year: 1994
Title: Structure of the Escherichia coli signal transducing protein PII.
Authors: Cheah, E. / Carr, P.D. / Suffolk, P.M. / Vasudevan, S.G. / Dixon, N.E. / Ollis, D.L.
#1: Journal: FEBS Lett. / Year: 1994
Title: Escherichia Coli Pii Protein: Purification, Crystallization, and Oligomeric Structure
Authors: Vasudevan, S.G. / Gedye, C. / Dixon, N.E. / Cheah, U.E. / Carr, P.D. / Suffolk, P.M. / Jeffrey, P.D. / Ollis, D.L.
History
DepositionAug 4, 1994Processing site: BNL
Revision 1.0Aug 4, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIGNAL TRANSDUCING PROTEIN P2


Theoretical massNumber of molelcules
Total (without water)12,4431
Polymers12,4431
Non-polymers00
Water00
1
A: SIGNAL TRANSDUCING PROTEIN P2

A: SIGNAL TRANSDUCING PROTEIN P2

A: SIGNAL TRANSDUCING PROTEIN P2


Theoretical massNumber of molelcules
Total (without water)37,3303
Polymers37,3303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7650 Å2
ΔGint-34 kcal/mol
Surface area15630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.600, 61.600, 56.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsTHE TWO TRANSFORMATIONS PRESENTED BELOW WILL GENERATE A TRIMER FROM THE SUBMITTED COORDINATES. THEY ARE CRYSTALLOGRAPHIC TRANSFORMATIONS. SYMTY1 1 -0.500000 0.866030 0.000000 -30.81050 SYMTY2 1 -0.866030 -0.500000 0.000000 53.36540 SYMTY3 1 0.000000 0.000000 1.000000 0.00000 SYMTY1 2 -0.500000 -0.866030 0.000000 30.81050 SYMTY2 2 0.866030 -0.500000 0.000000 53.36540 SYMTY3 2 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein SIGNAL TRANSDUCING PROTEIN P2


Mass: 12443.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A9Z1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Vasudevan, S.G., (1994) FEBS Lett., 337, 255.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
21 Mphosphate1drop
32 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 6578 / % possible obs: 89.5 % / Rmerge(I) obs: 0.025

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.24 / Rfactor obs: 0.24 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 0 0 872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.492
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.245 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS

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