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- PDB-3ncp: GlnK2 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 3ncp
TitleGlnK2 from Archaeoglobus fulgidus
ComponentsNitrogen regulatory protein P-II (GlnB-2)
KeywordsSIGNALING PROTEIN / PII signaling proteins / nucleotide binding / GlnK / GlnB
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytoplasm
Similarity search - Function
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 ...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
Nitrogen regulatory protein GlnK2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHelfmann, S. / Lue, W. / Litz, C. / Andrade, S.L.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Cooperative binding of MgATP and MgADP in the trimeric P(II) protein GlnK2 from Archaeoglobus fulgidus.
Authors: Helfmann, S. / Lu, W. / Litz, C. / Andrade, S.L.
History
DepositionJun 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2887
Polymers53,1814
Non-polymers1063
Water3,081171
1
A: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9926
Polymers39,8863
Non-polymers1063
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 area8010 Å2
ΔGint-88 kcal/mol
Surface area15410 Å2
MethodPISA
2
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9926
Polymers39,8863
Non-polymers1063
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 area6760 Å2
ΔGint-48 kcal/mol
Surface area13640 Å2
MethodPISA
3
C: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9926
Polymers39,8863
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area7000 Å2
ΔGint-45 kcal/mol
Surface area12580 Å2
MethodPISA
4
D: Nitrogen regulatory protein P-II (GlnB-2)

D: Nitrogen regulatory protein P-II (GlnB-2)

D: Nitrogen regulatory protein P-II (GlnB-2)


Theoretical massNumber of molelcules
Total (without water)39,8863
Polymers39,8863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6610 Å2
ΔGint-26 kcal/mol
Surface area12460 Å2
MethodPISA
5
A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,98512
Polymers79,7726
Non-polymers2136
Water1086
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 area17830 Å2
ΔGint-150 kcal/mol
Surface area25990 Å2
MethodPISA
6
C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8789
Polymers79,7726
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area15580 Å2
ΔGint-86 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.000, 91.000, 64.432
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11B-120-

CL

21C-120-

CL

31B-128-

HOH

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Components

#1: Protein
Nitrogen regulatory protein P-II (GlnB-2)


Mass: 13295.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1747, glnK2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O28527
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, Na Acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.5 Å / Num. all: 24946 / Num. obs: 24887 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.45 % / Biso Wilson estimate: 46.61 Å2 / Rmerge(I) obs: 0.0612 / Rsym value: 0.0612 / Net I/σ(I): 6.38
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.3662 / Mean I/σ(I) obs: 2.91 / Num. unique all: 2712 / Rsym value: 0.3662 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
BUSTER2.9.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GNK

2gnk


Resolution: 2.35→37.17 Å / Cor.coef. Fo:Fc: 0.9375 / Cor.coef. Fo:Fc free: 0.9326 / SU R Cruickshank DPI: 0.252 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1225 4.92 %RANDOM
Rwork0.2008 ---
obs0.2018 24875 99.88 %-
all-24887 --
Displacement parametersBiso mean: 43.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.3256 Å20 Å20 Å2
2--0.3256 Å20 Å2
3----0.6512 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: LAST / Resolution: 2.35→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 3 171 3314
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0131722
X-RAY DIFFRACTIONt_angle_deg1.3642622
X-RAY DIFFRACTIONt_dihedral_angle_d11632
X-RAY DIFFRACTIONt_trig_c_planes872
X-RAY DIFFRACTIONt_gen_planes4495
X-RAY DIFFRACTIONt_it317220
X-RAY DIFFRACTIONt_nbd85
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion20.6
X-RAY DIFFRACTIONt_chiral_improper_torsion4265
X-RAY DIFFRACTIONt_ideal_dist_contact37604
LS refinement shellResolution: 2.35→2.45 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2096 153 4.97 %
Rwork0.1643 2926 -
all0.1666 3079 -
obs--99.88 %

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