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- PDB-3t9z: A. fulgidus GlnK3, ligand-free -

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Basic information

Entry
Database: PDB / ID: 3t9z
TitleA. fulgidus GlnK3, ligand-free
ComponentsNitrogen regulatory protein P-II (GlnB-3)
KeywordsSIGNALING PROTEIN / PII-family / regulator / Amt3
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol
Similarity search - Function
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 ...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
CITRATE ANION / Nitrogen regulatory protein GlnK3
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMaier, S. / Schleberger, P. / Lue, W. / Wacker, T. / Pflueger, T. / Litz, C. / Andrade, S.L.A.
CitationJournal: Plos One / Year: 2011
Title: Mechanism of disruption of the Amt-GlnK complex by P(II)-mediated sensing of 2-oxoglutarate.
Authors: Maier, S. / Schleberger, P. / Lu, W. / Wacker, T. / Pfluger, T. / Litz, C. / Andrade, S.L.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Nitrogen regulatory protein P-II (GlnB-3)
B: Nitrogen regulatory protein P-II (GlnB-3)
C: Nitrogen regulatory protein P-II (GlnB-3)
D: Nitrogen regulatory protein P-II (GlnB-3)
E: Nitrogen regulatory protein P-II (GlnB-3)
F: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1757
Polymers78,9856
Non-polymers1891
Water6,359353
1
A: Nitrogen regulatory protein P-II (GlnB-3)
B: Nitrogen regulatory protein P-II (GlnB-3)
C: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6824
Polymers39,4933
Non-polymers1891
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-27 kcal/mol
Surface area13000 Å2
MethodPISA
2
D: Nitrogen regulatory protein P-II (GlnB-3)
E: Nitrogen regulatory protein P-II (GlnB-3)
F: Nitrogen regulatory protein P-II (GlnB-3)


Theoretical massNumber of molelcules
Total (without water)39,4933
Polymers39,4933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-26 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.350, 92.760, 88.410
Angle α, β, γ (deg.)90.00, 133.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nitrogen regulatory protein P-II (GlnB-3) / GlnK3


Mass: 13164.234 Da / Num. of mol.: 6 / Fragment: UNP residues 12-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1750, glnK3 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: O28524
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 17% PEG3350, 0.1 M sodium citrate buffer, pH 3.5, 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 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Bartels / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→64.4 Å / Num. all: 64689 / Num. obs: 63525 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 29.29 Å2 / Rsym value: 0.048 / Net I/σ(I): 11
Reflection shellResolution: 1.82→1.92 Å / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.288 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
BUSTER2.9.6refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O8W

3o8w


Resolution: 1.82→26.65 Å / Cor.coef. Fo:Fc: 0.9218 / Cor.coef. Fo:Fc free: 0.9047 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.117 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 3207 5.07 %RANDOM
Rwork0.2072 ---
all0.2087 64592 --
obs0.2087 63307 98.01 %-
Displacement parametersBiso mean: 40.66 Å2
Baniso -1Baniso -2Baniso -3
1-8.8749 Å20 Å21.8575 Å2
2---16.9262 Å20 Å2
3---8.0513 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.82→26.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 13 353 4668
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014339HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135811HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1652SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes615HARMONIC5
X-RAY DIFFRACTIONt_it4339HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion15.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion581SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5130SEMIHARMONIC4
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2554 250 5.31 %
Rwork0.2355 4458 -
all0.2366 4708 -
obs--98.01 %

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