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- PDB-4co5: Structure of PII signaling protein GlnZ from Azospirillum brasile... -

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Basic information

Entry
Database: PDB / ID: 4co5
TitleStructure of PII signaling protein GlnZ from Azospirillum brasilense in complex with tartrate
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
L(+)-TARTARIC ACID / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesAZOSPIRILLUM BRASILENSE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4372
Polymers12,2871
Non-polymers1501
Water1,982110
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)37,3126
Polymers36,8613
Non-polymers4503
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 area7270 Å2
ΔGint-42.6 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.700, 89.700, 108.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

21A-2030-

HOH

31A-2055-

HOH

41A-2095-

HOH

51A-2097-

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-TLA / L(+)-TARTARIC ACID / Tartaric acid


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


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.42 Å3/Da / Density % sol: 64.05 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 MM 2OG, 0.1 M HEPES PH 7.5, 0.8 M K/NA TARTRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 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: 1.8→44.45 Å / Num. obs: 15755 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.84 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.72 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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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: 1.8→44.45 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 788 5 %
Rwork0.1952 --
obs0.1967 15751 99.92 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.709 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4083 Å20 Å20 Å2
2---1.4083 Å20 Å2
3---2.8166 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 10 110 878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006773
X-RAY DIFFRACTIONf_angle_d0.9381042
X-RAY DIFFRACTIONf_dihedral_angle_d14.539278
X-RAY DIFFRACTIONf_chiral_restr0.071132
X-RAY DIFFRACTIONf_plane_restr0.005129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.91280.31351300.29752462X-RAY DIFFRACTION100
1.9128-2.06050.27621290.2272458X-RAY DIFFRACTION100
2.0605-2.26790.2361300.20252471X-RAY DIFFRACTION100
2.2679-2.5960.28021300.20092476X-RAY DIFFRACTION100
2.596-3.27060.22591330.1932514X-RAY DIFFRACTION100
3.2706-44.46360.19951360.17832582X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.2067 Å / Origin y: -0.2755 Å / Origin z: 39.9468 Å
111213212223313233
T0.2142 Å2-0.0094 Å20.0204 Å2-0.2116 Å2-0.02 Å2--0.1961 Å2
L1.3113 °2-0.4867 °20.376 °2-1.0232 °20.1636 °2--1.0435 °2
S0.0475 Å °0.1673 Å °0.0429 Å °-0.1472 Å °-0.0842 Å °-0.2027 Å °0.0555 Å °0.0857 Å °0.0114 Å °
Refinement TLS groupSelection details: CHAIN A AND RESSEQ 1:1109

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