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- PDB-4cny: Structure of PII signaling protein GlnZ from Azospirillum brasilense -

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Basic information

Entry
Database: PDB / ID: 4cny
TitleStructure of PII signaling protein GlnZ from Azospirillum brasilense
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
PHOSPHATE ION / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesAZOSPIRILLUM BRASILENSE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / 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_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_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

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Assembly

Deposited unit
A: PII-LIKE PROTEIN PZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5724
Polymers12,2871
Non-polymers2853
Water3,189177
1
A: PII-LIKE PROTEIN PZ
hetero molecules

A: PII-LIKE PROTEIN PZ
hetero molecules

A: PII-LIKE PROTEIN PZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,71612
Polymers36,8613
Non-polymers8559
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area6870 Å2
ΔGint-69.7 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.630, 87.630, 87.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1111-

PO4

21A-1111-

PO4

31A-1112-

PO4

41A-1112-

PO4

51A-2098-

HOH

61A-2100-

HOH

71A-2175-

HOH

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Components

#1: Protein PII-LIKE PROTEIN PZ


Mass: 12287.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AZOSPIRILLUM BRASILENSE (bacteria) / References: UniProt: P70731
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.4 M AMMONIUM PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2008 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.1→35.78 Å / Num. obs: 44969 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.59 % / Biso Wilson estimate: 12.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % 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 1GNK

1gnk


Resolution: 1.2→35.775 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 12.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 2001 5.7 %
Rwork0.147 --
obs0.1483 34977 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.208 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.9709 Å20 Å20 Å2
2---0.9709 Å20 Å2
3----0.9709 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms711 0 15 177 903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006734
X-RAY DIFFRACTIONf_angle_d1.163988
X-RAY DIFFRACTIONf_dihedral_angle_d12.414272
X-RAY DIFFRACTIONf_chiral_restr0.066120
X-RAY DIFFRACTIONf_plane_restr0.005122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2001-1.23010.15671420.15322323X-RAY DIFFRACTION100
1.2301-1.26330.20271430.16472362X-RAY DIFFRACTION100
1.2633-1.30050.17421420.1542310X-RAY DIFFRACTION100
1.3005-1.34250.16091420.13312354X-RAY DIFFRACTION100
1.3425-1.39050.15461440.13442344X-RAY DIFFRACTION100
1.3905-1.44620.15161450.12332323X-RAY DIFFRACTION100
1.4462-1.5120.13931430.10942358X-RAY DIFFRACTION100
1.512-1.59170.14241410.10422338X-RAY DIFFRACTION100
1.5917-1.69140.1431440.10942361X-RAY DIFFRACTION100
1.6914-1.8220.14311380.11992349X-RAY DIFFRACTION100
1.822-2.00530.18531440.12862365X-RAY DIFFRACTION100
2.0053-2.29550.17621390.14992361X-RAY DIFFRACTION100
2.2955-2.89190.19451440.15882370X-RAY DIFFRACTION100
2.8919-35.79070.17491500.17252458X-RAY DIFFRACTION100

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