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- PDB-4ush: Nitrogen regulatory protein PII from Chlamydomonas reinhardtii in... -

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Basic information

Entry
Database: PDB / ID: 4ush
TitleNitrogen regulatory protein PII from Chlamydomonas reinhardtii in unliganded state
ComponentsNITROGEN REGULATORY PROTEIN PII
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding
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 PII
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChellamuthu, V.R. / Forchhammer, K. / Hartmann, M.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: A Widespread Glutamine-Sensing Mechanism in the Plant Kingdom.
Authors: Chellamuthu, V.R. / Ermilova, E. / Lapina, T. / Luddecke, J. / Minaeva, E. / Herrmann, C. / Hartmann, M.D. / Forchhammer, K.
History
DepositionJul 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITROGEN REGULATORY PROTEIN PII
B: NITROGEN REGULATORY PROTEIN PII
C: NITROGEN REGULATORY PROTEIN PII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5997
Polymers51,2153
Non-polymers3844
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-137.9 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.980, 89.780, 45.940
Angle α, β, γ (deg.)90.00, 97.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NITROGEN REGULATORY PROTEIN PII


Mass: 17071.666 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 63-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A8JI83
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.7 Å3/Da / Density % sol: 27 % / Description: NONE
Crystal growDetails: 0.15 M (NH4)2SO4, 0.1 M HEPES, PH 7.0, 20% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→37.8 Å / Num. obs: 44312 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.64 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.52 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.81 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XZW

2xzw


Resolution: 1.6→37.79 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.668 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 2216 5 %RANDOM
Rwork0.16959 ---
obs0.17173 42096 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.497 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.53 Å2
2--1.13 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 20 255 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192507
X-RAY DIFFRACTIONr_bond_other_d0.0010.022501
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9713407
X-RAY DIFFRACTIONr_angle_other_deg0.88135721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68821.71799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36115412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6561524
X-RAY DIFFRACTIONr_chiral_restr0.1220.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 151 -
Rwork0.273 2874 -
obs--92.06 %
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)
11.66040.60691.39060.4510.46554.59240.02040.0027-0.1448-0.12290.009-0.10270.1856-0.0019-0.02940.10560.00020.06530.0153-0.00130.077314.4281-3.10959.0269
22.07851.1237-0.01623.45960.69151.5159-0.0631-0.0323-0.0943-0.09940.0105-0.01050.00310.04680.05260.05990.00180.05370.0020.00390.05286.8889-7.170526.2364
33.0452-0.9057-0.12861.39150.64871.55110.00880.03240.1243-0.057-0.0117-0.112-0.08660.05330.0030.0598-0.00230.05370.00290.00380.06174.296510.234519.0795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 125
2X-RAY DIFFRACTION2B6 - 124
3X-RAY DIFFRACTION3C9 - 127

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