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- PDB-4co1: Structure of PII signaling protein GlnZ from Azospirillum brasile... -

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Basic information

Entry
Database: PDB / ID: 4co1
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 / 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_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
B: PII-LIKE PROTEIN PZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4294
Polymers24,5742
Non-polymers8542
Water4,143230
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 area8790 Å2
ΔGint-50.9 kcal/mol
Surface area14780 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)38,1436
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 area8650 Å2
ΔGint-56.9 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.430, 89.430, 67.370
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-2083-

HOH

21A-2102-

HOH

31B-2020-

HOH

41B-2040-

HOH

51B-2078-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.11 Å3/Da / Density % sol: 41.81 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 MM ADP, 0.1 M NA HEPES PH 7.5, 25% PEG 1000, 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
Reflection twinOperator: h,-h-k,-l / Fraction: 0.45
ReflectionResolution: 1.5→30.9 Å / Num. obs: 32015 / % possible obs: 88.5 % / Observed criterion σ(I): 2 / Redundancy: 5.32 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.78 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.3 / % 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: 1.5→30.89 Å / σ(F): 2.01 / Phase error: 21.67 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1712 1602 5 %
Rwork0.139 --
obs0.1463 32014 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.275 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 54 230 1907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071717
X-RAY DIFFRACTIONf_angle_d1.0232335
X-RAY DIFFRACTIONf_dihedral_angle_d14.591622
X-RAY DIFFRACTIONf_chiral_restr0.059289
X-RAY DIFFRACTIONf_plane_restr0.003286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5005-1.54890.29591460.2922758X-RAY DIFFRACTION94
1.5489-1.60420.30651470.27812797X-RAY DIFFRACTION95
1.6042-1.66850.32571470.27892788X-RAY DIFFRACTION95
1.6685-1.74440.28991440.28132748X-RAY DIFFRACTION95
1.7444-1.83640.25791470.25382779X-RAY DIFFRACTION95
1.8364-1.95140.24431470.22112800X-RAY DIFFRACTION95
1.9514-2.1020.24681460.18642767X-RAY DIFFRACTION95
2.102-2.31350.181440.16192751X-RAY DIFFRACTION95
2.3135-2.64810.19551480.142800X-RAY DIFFRACTION95
2.6481-3.33570.13211460.10312772X-RAY DIFFRACTION95
3.3357-30.89630.09861390.07442640X-RAY DIFFRACTION90

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