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- PDB-1gnk: GLNK, A SIGNAL PROTEIN FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1gnk
TitleGLNK, A SIGNAL PROTEIN FROM E. COLI
ComponentsPROTEIN (GLNK)
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of nitrogen utilization / regulation of nitrogen utilization / enzyme regulator activity / ATP binding / identical protein binding / plasma membrane / 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 GlnK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, Y. / Cheah, E. / Carr, P.D. / Vanheeswijk, W.C. / Westerhoff, H.V. / Vasudevan, S.G. / Ollis, D.L.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: GlnK, a PII-homologue: structure reveals ATP binding site and indicates how the T-loops may be involved in molecular recognition.
Authors: Xu, Y. / Cheah, E. / Carr, P.D. / van Heeswijk, W.C. / Westerhoff, H.V. / Vasudevan, S.G. / Ollis, D.L.
History
DepositionJul 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GLNK)
B: PROTEIN (GLNK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7454
Polymers24,5522
Non-polymers1922
Water2,360131
1
A: PROTEIN (GLNK)
hetero molecules

A: PROTEIN (GLNK)
hetero molecules

A: PROTEIN (GLNK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1176
Polymers36,8293
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPQS
2
B: PROTEIN (GLNK)
hetero molecules

B: PROTEIN (GLNK)
hetero molecules

B: PROTEIN (GLNK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1176
Polymers36,8293
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
MethodPQS
Unit cell
Length a, b, c (Å)85.530, 85.530, 85.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-137-

HOH

21B-138-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.32092, -0.53527, -0.78134), (0.53975, 0.78126, -0.31353), (0.77826, -0.32111, 0.53963)
Vector: 39.94856, 45.4587, 2.59596)

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Components

#1: Protein PROTEIN (GLNK)


Mass: 12276.192 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Plasmid: PNV102 / Strain: RB9040 / References: UniProt: P0AC55
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.5 / Details: 30% MPD, 0.2M CH3COONH4, 0.1M CACODYLATE, PH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Macpherson, K.H.R., (1998) Acta Crystallog. sect., D54, 996.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-13.3 mg/mlprotein1drop
230 %MPD1reservoir
30.2 Mammonium acetate1reservoir
40.1 Mcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 14384 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.182
Reflection
*PLUS
Num. measured all: 97474

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.01refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→6 Å / Data cutoff low absF: 15 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1379 10 %RANDOM
Rwork0.189 ---
obs0.189 14077 88.5 %-
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 10 131 1701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.664
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
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.276 85 6.3 %
Rwork0.242 880 -
obs--71.9 %
Xplor fileSerial no: 3 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.01 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / % reflection Rfree: 6.3 % / Rfactor Rwork: 0.242

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