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- PDB-7o4x: Crystal structure of the PII-like protein PotN from Lentilactobac... -

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Basic information

Entry
Database: PDB / ID: 7o4x
TitleCrystal structure of the PII-like protein PotN from Lentilactobacillus hilgardii
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN
Function / homologyAlpha-Beta Plaits - #120 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesLactobacillus brevis subsp. gravesensis ATCC 27305 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHeim, C. / Hartmann, M.D.
CitationJournal: Febs J. / Year: 2022
Title: PotN represents a novel energy-state sensing PII subfamily, occurring in firmicutes.
Authors: Iskhakova, Z.I. / Zhuravleva, D.E. / Heim, C. / Hartmann, M.D. / Laykov, A.V. / Forchhammer, K. / Kayumov, A.R.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1872
Polymers13,7601
Non-polymers4271
Water1,38777
1
A: Nitrogen regulatory protein P-II
hetero molecules

A: Nitrogen regulatory protein P-II
hetero molecules

A: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5616
Polymers41,2803
Non-polymers1,2823
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10050 Å2
ΔGint-66 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.151, 80.151, 79.484
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-356-

HOH

21A-368-

HOH

31A-372-

HOH

41A-373-

HOH

51A-374-

HOH

61A-377-

HOH

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Components

#1: Protein Nitrogen regulatory protein P-II


Mass: 13759.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis subsp. gravesensis ATCC 27305 (bacteria)
Gene: HMPREF0496_1931 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C2D309
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.56 M Tri-Na Citrate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.65→40.11 Å / Num. obs: 18721 / % possible obs: 100 % / Redundancy: 26.19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.093 / Net I/σ(I): 21.4
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 24.71 % / Rmerge(I) obs: 2.03 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2935 / CC1/2: 0.72 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EG1

2eg1


Resolution: 1.65→40.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.461 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19945 922 4.9 %RANDOM
Rwork0.17922 ---
obs0.18022 17799 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.65→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms779 0 27 77 883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.013840
X-RAY DIFFRACTIONr_bond_other_d0.0010.017845
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.6351143
X-RAY DIFFRACTIONr_angle_other_deg1.4371.5811953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.92922.43237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99815164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.28156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02161
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7052.016420
X-RAY DIFFRACTIONr_mcbond_other1.7012.011419
X-RAY DIFFRACTIONr_mcangle_it2.7013524
X-RAY DIFFRACTIONr_mcangle_other2.6983.006525
X-RAY DIFFRACTIONr_scbond_it2.8322.377420
X-RAY DIFFRACTIONr_scbond_other2.8332.377420
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4123.429615
X-RAY DIFFRACTIONr_long_range_B_refined7.28724.248809
X-RAY DIFFRACTIONr_long_range_B_other7.21623.798802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 69 -
Rwork0.381 1275 -
obs--99.41 %
Refinement TLS params.Method: refined / Origin x: 28.8223 Å / Origin y: -23.1177 Å / Origin z: 5.4396 Å
111213212223313233
T0.0104 Å2-0.0068 Å2-0.0097 Å2-0.0408 Å2-0.0044 Å2--0.037 Å2
L2.5987 °2-0.2596 °2-0.1245 °2-2.0412 °2-0.0871 °2--2.321 °2
S0.0527 Å °0.0475 Å °-0.0318 Å °-0.0049 Å °-0.065 Å °0.2371 Å °0.0126 Å °-0.2811 Å °0.0123 Å °

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