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- PDB-4co4: Structure of PII signaling protein GlnZ from Azospirillum brasile... -

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Basic information

Entry
Database: PDB / ID: 4co4
TitleStructure of PII signaling protein GlnZ from Azospirillum brasilense in complex with adenosine triphosphate
ComponentsPII-LIKE PROTEIN PZ
KeywordsSIGNALING PROTEIN / GLNK-LIKE
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / metal ion 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
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesAZOSPIRILLUM BRASILENSE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTruan, D. / Li, X.-D. / Winkler, F.K.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structure and Thermodynamics of Effector Molecule Binding to the Nitrogen Signal Transduction Pii Protein Glnz from Azospirillum Brasilense.
Authors: Truan, D. / Bjelic, S. / Li, X. / Winkler, F.K.
History
DepositionJan 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PII-LIKE PROTEIN PZ
B: PII-LIKE PROTEIN PZ
C: PII-LIKE PROTEIN PZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5089
Polymers36,8613
Non-polymers1,6466
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-59.9 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.681, 58.950, 90.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PII-LIKE PROTEIN PZ


Mass: 12287.109 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) AZOSPIRILLUM BRASILENSE (bacteria) / References: UniProt: P70731
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 1.94 Å3/Da / Density % sol: 36.71 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15 MM ATP, 0.2 M NACL, 0.1 M PHOSPHATE CITRATE PH 4.2, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2009
Details: VERTICALLY COLLIMATING MIRROR FOLLOWED BY A BARTELS MONOCHROMATOR AND A TOROIDAL MIRROR
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→46.16 Å / Num. obs: 45979 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.73 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.1
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 6.37 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.5 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CNY

4cny


Resolution: 1.5→46.155 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 20.77 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.206 2299 5 %
Rwork0.1661 --
obs0.1681 45974 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→46.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 100 320 2445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052191
X-RAY DIFFRACTIONf_angle_d0.9322985
X-RAY DIFFRACTIONf_dihedral_angle_d15.946812
X-RAY DIFFRACTIONf_chiral_restr0.059367
X-RAY DIFFRACTIONf_plane_restr0.003356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53270.30531240.24462359X-RAY DIFFRACTION86
1.5327-1.56830.29271340.22532550X-RAY DIFFRACTION94
1.5683-1.60750.30261410.20482685X-RAY DIFFRACTION99
1.6075-1.6510.28961440.19052734X-RAY DIFFRACTION100
1.651-1.69960.27861450.17562746X-RAY DIFFRACTION100
1.6996-1.75440.24151430.16862716X-RAY DIFFRACTION100
1.7544-1.81710.21111440.15512750X-RAY DIFFRACTION100
1.8171-1.88990.23361450.15482740X-RAY DIFFRACTION100
1.8899-1.97590.20541460.15232776X-RAY DIFFRACTION100
1.9759-2.08010.21191440.1512743X-RAY DIFFRACTION100
2.0801-2.21040.22261450.14922752X-RAY DIFFRACTION100
2.2104-2.38110.19611460.14212773X-RAY DIFFRACTION100
2.3811-2.62070.19861460.15192777X-RAY DIFFRACTION100
2.6207-2.99980.19731480.16642807X-RAY DIFFRACTION100
2.9998-3.77920.1681480.16152815X-RAY DIFFRACTION99
3.7792-46.17650.17421560.17632952X-RAY DIFFRACTION99

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