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- PDB-2o66: Crystal Structure of Arabidopsis thaliana PII bound to citrate -

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Basic information

Entry
Database: PDB / ID: 2o66
TitleCrystal Structure of Arabidopsis thaliana PII bound to citrate
ComponentsPII protein
KeywordsBIOSYNTHETIC PROTEIN / REGULATION OF NITROGEN AND CARBON METABOLISM
Function / homology
Function and homology information


acetylglutamate kinase regulator activity / regulation of arginine biosynthetic process via ornithine / anthocyanin-containing compound biosynthetic process / chloroplast thylakoid / regulation of fatty acid biosynthetic process / response to sucrose / regulation of nitrogen utilization / plastid / response to light stimulus / chloroplast ...acetylglutamate kinase regulator activity / regulation of arginine biosynthetic process via ornithine / anthocyanin-containing compound biosynthetic process / chloroplast thylakoid / regulation of fatty acid biosynthetic process / response to sucrose / regulation of nitrogen utilization / plastid / response to light stimulus / chloroplast / magnesium ion binding / ATP binding / cytosol
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
CITRATE ANION / Nitrogen regulatory protein P-II homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMizuno, Y. / Berenger, B. / Moorhead, G.B.G. / Ng, K.K.S.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal Structure of Arabidopsis PII Reveals Novel Structural Elements Unique to Plants.
Authors: Mizuno, Y. / Berenger, B. / Moorhead, G.B. / Ng, K.K.
History
DepositionDec 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: PII protein
B: PII protein
C: PII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9076
Polymers44,3403
Non-polymers5673
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-26 kcal/mol
Surface area13680 Å2
MethodPISA
2
A: PII protein
B: PII protein
C: PII protein
hetero molecules

A: PII protein
B: PII protein
C: PII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,81412
Polymers88,6796
Non-polymers1,1356
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20730 Å2
ΔGint-62 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.709, 66.752, 61.743
Angle α, β, γ (deg.)90.00, 118.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PII protein / P II nitrogen sensing protein GLB I / At4g01900


Mass: 14779.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g01900, T7B11.16 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami pLysS / References: UniProt: Q9ZST4
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.89 Å3/Da / Density % sol: 34.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M ammonium citrate, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 14, 2005 / Details: Osmic multilayer
RadiationMonochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 25717 / Num. obs: 25717 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 5 / Rsym value: 0.244 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1UL3

1ul3


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.23 / SU ML: 0.096 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.165 / ESU R Free: 0.144 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22406 1323 5.1 %RANDOM
Rwork0.19106 ---
all0.19278 24505 --
obs0.19278 24505 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-0.3 Å2
2---0.37 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 39 153 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222572
X-RAY DIFFRACTIONr_angle_refined_deg1.0271.9873451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85523.301103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83615501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5561524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021846
X-RAY DIFFRACTIONr_nbd_refined0.1730.21196
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0720.215
X-RAY DIFFRACTIONr_mcbond_it1.67321635
X-RAY DIFFRACTIONr_mcangle_it2.5632.52587
X-RAY DIFFRACTIONr_scbond_it3.5153.51041
X-RAY DIFFRACTIONr_scangle_it5.4474.5864
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 105 -
Rwork0.225 1681 -
obs--94.05 %

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