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

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Basic information

Entry
Database: PDB / ID: 4usi
TitleNitrogen regulatory protein PII from Chlamydomonas reinhardtii in complex with MgATP and 2-oxoglutarate
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 / 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 / Nitrogen regulatory protein PII
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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_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_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_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)52,66610
Polymers51,2153
Non-polymers1,4517
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-106.8 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.040, 90.170, 46.180
Angle α, β, γ (deg.)90.00, 96.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 292 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→37.9 Å / Num. obs: 59345 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.6
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.02 / % possible all: 93.5

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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: 1.45→37.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.846 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21587 2971 5 %RANDOM
Rwork0.18546 ---
obs0.187 56367 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20.8 Å2
2---1.51 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.45→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 89 285 2914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192761
X-RAY DIFFRACTIONr_bond_other_d0.0020.022705
X-RAY DIFFRACTIONr_angle_refined_deg2.4623774
X-RAY DIFFRACTIONr_angle_other_deg1.00836206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79921.942103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52515441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9121524
X-RAY DIFFRACTIONr_chiral_restr0.1530.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
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: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 191 -
Rwork0.334 3816 -
obs--90.41 %
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)
11.34910.15760.08921.3082-0.04892.21120.01460.048-0.0906-0.08830.0057-0.05130.04460.0631-0.02030.0735-0.0083-0.02840.2197-0.00740.021313.1419-1.27038.2471
21.29141.09850.22491.93550.09041.6817-0.0279-0.0028-0.0873-0.08880.0099-0.07930.04910.06260.0180.07840.009-0.03960.2224-0.00080.03197.1978-8.08425.1239
32.0495-0.7274-0.02091.68390.41190.8690.0239-0.14020.1030.06630.0007-0.0243-0.080.0319-0.02460.0867-0.0084-0.03910.23370.00230.03574.291910.18219.2527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 153
2X-RAY DIFFRACTION2B6 - 153
3X-RAY DIFFRACTION3C7 - 152

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