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- PDB-3n5b: The complex of PII and PipX from Anabaena -

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Basic information

Entry
Database: PDB / ID: 3n5b
TitleThe complex of PII and PipX from Anabaena
Components
  • Asr0485 protein
  • Nitrogen regulatory protein P-II
KeywordsTRANSCRIPTION REGULATOR / PII / PipX / signal transducer
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding
Similarity search - Function
Protein of unknown function (DUF3539) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #870 / PII-interacting protein X, cyanobacteria / PII-interacting protein X / 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 ...Protein of unknown function (DUF3539) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #870 / PII-interacting protein X, cyanobacteria / PII-interacting protein X / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / SH3 type barrels. / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Asr0485 protein / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesNostoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiang, Y.-L. / Zhao, M.-X. / Xu, B.-Y. / Chen, Y.-X. / Zhang, C.-C. / Zhou, C.-Z.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the cyanobacterial signal transduction protein PII in complex with PipX.
Authors: Zhao, M.-X. / Jiang, Y.-L. / Xu, B.-Y. / Chen, Y.-X. / Zhang, C.-C. / Zhou, C.-Z.
History
DepositionMay 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
B: Asr0485 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3325
Polymers25,7122
Non-polymers6193
Water2,396133
1
A: Nitrogen regulatory protein P-II
B: Asr0485 protein
hetero molecules

A: Nitrogen regulatory protein P-II
B: Asr0485 protein
hetero molecules

A: Nitrogen regulatory protein P-II
B: Asr0485 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,99515
Polymers77,1376
Non-polymers1,8589
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14540 Å2
ΔGint-55 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.645, 70.645, 88.544
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-128-

HOH

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Components

#1: Protein Nitrogen regulatory protein P-II / PII protein


Mass: 12510.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc (bacteria) / Strain: PCC 7120 / Gene: all2319, glnB / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9L422
#2: Protein Asr0485 protein / NtcA-interacting protein


Mass: 13201.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc (bacteria) / Strain: PCC 7120 / Gene: asr0485 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8YZH5
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6M ammonium sulfate, 0.1M Tris-Cl pH8.5, 6.4% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9194 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 1.9→88.54 Å / Num. obs: 20553 / % possible obs: 99.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1980

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QY7

1qy7


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.394 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24507 1052 5.1 %RANDOM
Rwork0.19783 ---
obs0.20014 19435 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 37 133 1772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221660
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9872238
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32123.65982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66915312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2231517
X-RAY DIFFRACTIONr_chiral_restr0.1140.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021218
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9821.5978
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7721586
X-RAY DIFFRACTIONr_scbond_it2.4673682
X-RAY DIFFRACTIONr_scangle_it4.0534.5652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 65 -
Rwork0.24 1386 -
obs--96.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9755-0.1057-0.22861.7198-0.26782.7783-0.0047-0.2389-0.11780.2412-0.00860.18190.0572-0.41580.01330.2149-0.00190.04510.29710.00860.027424.52819.18632.154
25.091-0.33432.75062.12480.02712.16940.1117-0.1057-0.2339-0.08820.02230.13940.08-0.1447-0.1340.181-0.0167-0.00820.22420.01150.08116.87415.48.969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2B6 - 91

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