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- PDB-2pii: PII, GLNB PRODUCT -

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Basic information

Entry
Database: PDB / ID: 2pii
TitlePII, GLNB PRODUCT
ComponentsPII
KeywordsSIGNAL TRANSDUCTION 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: 1.9 Å
AuthorsCarr, P.D. / Cheah, E. / Suffolk, P.M. / Ollis, D.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-ray structure of the signal transduction protein from Escherichia coli at 1.9 A.
Authors: Carr, P.D. / Cheah, E. / 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, E. / Carr, P.D. / Suffolk, P.M. / Jeffrey, P.D. / Ollis, D.L.
#2: 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.
History
DepositionMay 2, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 21, 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: PII


Theoretical massNumber of molelcules
Total (without water)12,4431
Polymers12,4431
Non-polymers00
Water5,621312
1
A: PII

A: PII

A: PII


Theoretical massNumber of molelcules
Total (without water)37,3303
Polymers37,3303
Non-polymers00
Water543
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 area7500 Å2
ΔGint-37 kcal/mol
Surface area16100 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
Components on special symmetry positions
IDModelComponents
11A-639-

HOH

21A-795-

HOH

31A-796-

HOH

41A-811-

HOH

51A-842-

HOH

61A-843-

HOH

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Components

#1: Protein PII / GLNB PRODUCT


Mass: 12443.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DERIVED FROM K12 / Gene: GLNB / Variant: AN1459 / Plasmid: PCG646 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9Z1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 53 %
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
ReflectionNum. obs: 11079 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. measured all: 45387 / Rmerge(I) obs: 0.071

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.132 -
obs0.132 7736
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 0 312 1184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.98
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
Rfactor obs: 0.132 / Rfactor Rwork: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS

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