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- PDB-5l9n: Structure of uridylylated GlnB from Escherichia coli bound to ATP -

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Basic information

Entry
Database: PDB / ID: 5l9n
TitleStructure of uridylylated GlnB from Escherichia coli bound to ATP
ComponentsNitrogen regulatory protein P-II 1
KeywordsSIGNALING PROTEIN / Uridylylation / PII protein / nitrogen metabolism / GlnK
Function / homology
Function and homology information


regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / small molecule binding / enzyme activator activity / enzyme regulator 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 / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / 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 / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / 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
ADENOSINE-5'-TRIPHOSPHATE / Nitrogen regulatory protein P-II 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsRubio, V. / Palanca, C.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish GovernmentBFU2011-30407 Spain
Spanish GovernmentBFU2014-58229-P Spain
CitationJournal: Environ Microbiol Rep / Year: 2017
Title: Effects of T-loop modification on the PII-signalling protein: structure of uridylylated Escherichia coli GlnB bound to ATP.
Authors: Palanca, C. / Rubio, V.
History
DepositionJun 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen regulatory protein P-II 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9753
Polymers12,4431
Non-polymers5312
Water66737
1
A: Nitrogen regulatory protein P-II 1
hetero molecules

A: Nitrogen regulatory protein P-II 1
hetero molecules

A: Nitrogen regulatory protein P-II 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9259
Polymers37,3303
Non-polymers1,5946
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area9140 Å2
ΔGint-37 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.868, 88.868, 88.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-332-

HOH

31A-333-

HOH

41A-335-

HOH

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Components

#1: Protein Nitrogen regulatory protein P-II 1


Mass: 12443.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: glnB, b2553, JW2537 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9Z1
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0,1 M NaAcetate pH 4.6, 20 mM CaCl2, 30% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.9→44.4 Å / Num. obs: 9346 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.7
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.618 / Num. unique all: 586

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PIL

1pil


Resolution: 1.901→28.103 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2232 449 4.81 %
Rwork0.1837 --
obs0.1855 9342 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→28.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 32 37 776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008760
X-RAY DIFFRACTIONf_angle_d1.2431038
X-RAY DIFFRACTIONf_dihedral_angle_d16.254289
X-RAY DIFFRACTIONf_chiral_restr0.04130
X-RAY DIFFRACTIONf_plane_restr0.006125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-2.17570.28041580.22632911X-RAY DIFFRACTION99
2.1757-2.74080.24681560.21772928X-RAY DIFFRACTION100
2.7408-28.1030.19941350.16363054X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2125-0.34830.27771.2318-0.52120.6318-0.0869-0.1707-0.24630.4248-0.0179-0.3590.31550.267400.2740.0535-0.05570.25420.00060.2299-15.625317.166-9.1667
20.01340.03160.11120.1169-0.34150.54140.12730.45880.56980.0039-0.00840.31080.3072-0.20530.00060.2691-0.03450.01130.27680.00870.2425-30.226720.4032-14.965
30.11190.28240.15020.51190.34260.15120.0134-0.1213-0.32120.15660.0396-0.32920.21070.01180.0010.24420.01060.01210.2724-0.03470.2609-19.98918.4436-14.3966
40.2296-0.1009-0.05070.24120.29760.3529-0.1444-0.1801-0.58140.65950.1311-0.84961.09950.60410.13180.43310.1994-0.0380.3604-0.04930.466-11.00729.5712-11.5357
50.46980.17920.52840.43090.23570.41610.1377-0.35210.11930.030.0417-0.0730.534-0.06510.00180.44970.01450.06060.3298-0.02160.3239-22.06589.3498-14.2399
60.10140.1085-0.02570.0174-0.05620.2091-0.2920.10340.066-0.1826-0.0149-0.092-0.35110.3435-0.00220.33410.04030.06530.3977-0.00650.6037-4.102627.2197-24.4746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 81 )
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 95 )
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 109 )

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