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- PDB-4co0: Structure of PII signaling protein GlnZ from Azospirillum brasile... -

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Basic information

Entry
Database: PDB / ID: 4co0
TitleStructure of PII signaling protein GlnZ from Azospirillum brasilense in complex with adenosine diphosphate
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-5'-DIPHOSPHATE / L(+)-TARTARIC ACID / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesAZOSPIRILLUM BRASILENSE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,5795
Polymers24,5742
Non-polymers1,0043
Water4,882271
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)38,1436
Polymers36,8613
Non-polymers1,2823
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area9280 Å2
ΔGint-55.5 kcal/mol
Surface area14440 Å2
MethodPISA
2
B: PII-LIKE PROTEIN PZ
hetero molecules

B: PII-LIKE PROTEIN PZ
hetero molecules

B: PII-LIKE PROTEIN PZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5939
Polymers36,8613
Non-polymers1,7326
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area9720 Å2
ΔGint-52.1 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.550, 86.550, 65.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2067-

HOH

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Components

#1: Protein PII-LIKE PROTEIN PZ


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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 1.91 Å3/Da / Density % sol: 35.73 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 MM MNCL2, 5MM 2OG, 5 MMATP, 0.2 M K/NA TARTRATE, 200% PEG 3350, 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: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2009
Details: VERTICALLY COLLIMATING MIRROR FOLLOWED BY A BARTELS MONOCHROMATOR AND 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: 1.4→29.87 Å / Num. obs: 35124 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 5.33 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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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: 1.4→29.868 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 1757 5 %
Rwork0.2105 --
obs0.2122 35124 97.99 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.083 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 23.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.4369 Å20 Å20 Å2
2---0.4369 Å20 Å2
3---0.8739 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 64 271 1931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051725
X-RAY DIFFRACTIONf_angle_d1.1782349
X-RAY DIFFRACTIONf_dihedral_angle_d16.881639
X-RAY DIFFRACTIONf_chiral_restr0.072289
X-RAY DIFFRACTIONf_plane_restr0.004288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43790.31381400.27772643X-RAY DIFFRACTION100
1.4379-1.48020.32071350.29442584X-RAY DIFFRACTION100
1.4802-1.52790.29261380.25822619X-RAY DIFFRACTION100
1.5279-1.58260.26231380.22382612X-RAY DIFFRACTION100
1.5826-1.64590.2521380.21542631X-RAY DIFFRACTION100
1.6459-1.72080.25441380.21032615X-RAY DIFFRACTION100
1.7208-1.81150.24491380.2042622X-RAY DIFFRACTION100
1.8115-1.9250.2571310.25472494X-RAY DIFFRACTION95
1.925-2.07360.24461350.2142555X-RAY DIFFRACTION98
2.0736-2.28220.27881330.22362533X-RAY DIFFRACTION97
2.2822-2.61230.21841360.20072587X-RAY DIFFRACTION99
2.6123-3.29050.23491380.19632615X-RAY DIFFRACTION100
3.2905-29.87470.22851190.19132257X-RAY DIFFRACTION86
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)
10.66550.0776-0.30591.26520.11420.99890.0559-0.01050.0104-0.0391-0.0422-0.0031-0.0537-0.06680.0160.0832-0.0019-0.00450.1047-0.00340.1003-8.36814.4005-4.5904
21.35040.2394-0.20360.61430.25431.385-0.14590.046-0.0957-0.00160.08430.05080.1795-0.06970.07070.1472-0.0035-0.01080.10610.00430.1223-0.3547-9.16826.1905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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