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- PDB-3ta2: A. fulgidus GlnK3, MgATP/2-OG complex -

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Basic information

Entry
Database: PDB / ID: 3ta2
TitleA. fulgidus GlnK3, MgATP/2-OG complex
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
2-OXOGLUTARIC ACID / ADENOSINE-5'-TRIPHOSPHATE / NICKEL (II) ION / Nitrogen regulatory protein GlnK3
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Sep 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,64314
Polymers39,4933
Non-polymers2,15011
Water6,215345
1
A: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,52512
Polymers39,4933
Non-polymers2,0339
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11760 Å2
ΔGint-71 kcal/mol
Surface area14660 Å2
MethodPISA
2
B: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules

B: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules

B: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,70215
Polymers39,4933
Non-polymers2,20912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area11730 Å2
ΔGint-73 kcal/mol
Surface area14640 Å2
MethodPISA
3
C: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,70215
Polymers39,4933
Non-polymers2,20912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12100 Å2
ΔGint-82 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.220, 79.220, 223.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

21C-241-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 13164.234 Da / Num. of mol.: 3 / 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

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Non-polymers , 5 types, 356 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% MPD, 0.2 M sodium chloride, 0.1 M sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
RadiationMonochromator: VariMax VHF Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.73 Å / Num. all: 33679 / Num. obs: 33612 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 17.54 Å2 / Rsym value: 0.135 / Net I/σ(I): 18
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.517 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
BUSTER2.9.6refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O8W

3o8w


Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.9463 / Cor.coef. Fo:Fc free: 0.9309 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.117 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1632 5.1 %RANDOM
Rwork0.1645 ---
all0.1662 33648 --
obs0.1662 32019 95.19 %-
Displacement parametersBiso mean: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.2895 Å20 Å20 Å2
2--0.2895 Å20 Å2
3----0.579 Å2
Refine analyzeLuzzati coordinate error obs: 0.176 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 128 345 3011
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012734HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.143685HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes387HARMONIC5
X-RAY DIFFRACTIONt_it2734HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion16.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion347SEMIHARMONIC5
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_contact3325SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.96 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2295 143 4.82 %
Rwork0.1921 2821 -
all0.1939 2964 -
obs--95.19 %

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