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- PDB-2o67: Crystal structure of Arabidopsis thaliana PII bound to malonate -

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Basic information

Entry
Database: PDB / ID: 2o67
TitleCrystal structure of Arabidopsis thaliana PII bound to malonate
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
MALONATE ION / Nitrogen regulatory protein P-II homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMizuno, Y.M. / 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)44,6466
Polymers44,3403
Non-polymers3063
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-20 kcal/mol
Surface area13890 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)89,29212
Polymers88,6796
Non-polymers6126
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19900 Å2
ΔGint-48 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.594, 66.726, 61.489
Angle α, β, γ (deg.)90.00, 118.41, 90.00
Int Tables number5
Space group name H-MC121
DetailsNative homotrimer is found in the asymmetric unit

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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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 M malonate, 0.1 M Na HEPES, pH 7.0, 10% glycerol, 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: Mar 21, 2006 / 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: 2.5→20 Å / Num. all: 11464 / Num. obs: 11464 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1139 / Rsym value: 0.517 / % possible all: 98.2

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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 2O66

2o66


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.716 / SU ML: 0.262 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.914 / ESU R Free: 0.326 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26567 552 4.8 %RANDOM
Rwork0.20088 ---
all0.20401 10903 --
obs0.20401 10903 99.63 %-
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: 44.622 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20.43 Å2
2---1.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 21 30 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.9783379
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.155311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43723.168101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0815493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9851524
X-RAY DIFFRACTIONr_chiral_restr0.0630.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.21041
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21719
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.71321606
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.642.52541
X-RAY DIFFRACTIONr_scbond_it3.433.51018
X-RAY DIFFRACTIONr_scangle_it5.2684.5838
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 30 -
Rwork0.249 777 -
obs-777 97.7 %

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