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- PDB-4co3: Structure of PII signaling protein GlnZ from Azospirillum brasile... -

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Basic information

Entry
Database: PDB / ID: 4co3
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
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
Similarity search - Component
Biological speciesAZOSPIRILLUM BRASILENSE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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.D. / 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 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / exptl_crystal_grow
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[3][3] / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.1Dec 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)25,5894
Polymers24,5742
Non-polymers1,0142
Water9,710539
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)38,3836
Polymers36,8613
Non-polymers1,5223
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 area9430 Å2
ΔGint-48.5 kcal/mol
Surface area14420 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)38,3836
Polymers36,8613
Non-polymers1,5223
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 area9210 Å2
ΔGint-44.7 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.700, 85.700, 67.130
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-2066-

HOH

21A-2070-

HOH

31A-2127-

HOH

41A-2179-

HOH

51A-2180-

HOH

61A-2181-

HOH

71B-2060-

HOH

81B-2122-

HOH

91B-2143-

HOH

101B-2199-

HOH

111B-2200-

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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 539 / 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: 1.93 Å3/Da / Density % sol: 36.29 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MES PH 6.5, 40% PEG 200, 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: 0.53
ReflectionResolution: 1.05→32.48 Å / Num. obs: 84996 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.21 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.3
Reflection shellResolution: 1.05→1.1 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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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: 1.05→32.477 Å / σ(F): 2 / Phase error: 21.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1991 4265 5 %
Rwork0.1592 --
obs0.1708 84994 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→32.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 62 539 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041648
X-RAY DIFFRACTIONf_angle_d0.7372231
X-RAY DIFFRACTIONf_dihedral_angle_d12.911607
X-RAY DIFFRACTIONf_chiral_restr0.043266
X-RAY DIFFRACTIONf_plane_restr0.003270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0501-1.06820.30222030.28463843X-RAY DIFFRACTION89
1.0682-1.08770.28632130.27714057X-RAY DIFFRACTION94
1.0877-1.10860.28512160.2734095X-RAY DIFFRACTION95
1.1086-1.13120.27942140.24764082X-RAY DIFFRACTION95
1.1312-1.15580.25652150.23964082X-RAY DIFFRACTION95
1.1558-1.18270.25742130.24174032X-RAY DIFFRACTION95
1.1827-1.21220.24662150.23574091X-RAY DIFFRACTION95
1.2122-1.2450.24112140.23884061X-RAY DIFFRACTION95
1.245-1.28160.24722140.24214072X-RAY DIFFRACTION95
1.2816-1.3230.25782150.24894088X-RAY DIFFRACTION95
1.323-1.37030.28532130.24924042X-RAY DIFFRACTION95
1.3703-1.42510.25582160.24114104X-RAY DIFFRACTION95
1.4251-1.48990.2562140.2344072X-RAY DIFFRACTION95
1.4899-1.56840.2382140.21954062X-RAY DIFFRACTION95
1.5684-1.66660.24782150.20634080X-RAY DIFFRACTION95
1.6666-1.79520.23222150.24084X-RAY DIFFRACTION95
1.7952-1.97570.21912140.16764081X-RAY DIFFRACTION95
1.9757-2.26110.18082150.13254085X-RAY DIFFRACTION95
2.2611-2.84680.16432150.10414070X-RAY DIFFRACTION95
2.8468-17.88660.15321870.08123551X-RAY DIFFRACTION83

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