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- PDB-2eg1: The crystal structure of PII protein -

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Basic information

Entry
Database: PDB / ID: 2eg1
TitleThe crystal structure of PII protein
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN / Nitrogen regulatory protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / 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
Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSakai, H. / Shinkai, A. / Kitamura, Y. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The crystal structure of PII protein
Authors: Sakai, H. / Shinkai, A. / Kitamura, Y. / Kuramitsu, S. / Yokoyama, S.
History
DepositionFeb 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7434
Polymers12,5161
Non-polymers2283
Water1,47782
1
A: Nitrogen regulatory protein P-II
hetero molecules

A: Nitrogen regulatory protein P-II
hetero molecules

A: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,22912
Polymers37,5473
Non-polymers6839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8390 Å2
ΔGint-146 kcal/mol
Surface area11870 Å2
MethodPISA
2
A: Nitrogen regulatory protein P-II
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)152,91848
Polymers150,18712
Non-polymers2,73136
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
MethodPQS
Unit cell
Length a, b, c (Å)81.04, 81.04, 81.04
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-501-

SO4

21A-501-

SO4

31A-601-

CL

41A-653-

HOH

51A-661-

HOH

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Components

#1: Protein Nitrogen regulatory protein P-II


Mass: 12515.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: glnB / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O66513
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.77 Å3/Da / Density % sol: 30.56 %
Crystal growTemperature: 291 K / pH: 5.3
Details: Citrate, Ammonium sulfate , pH5.3, microbatch method , temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 29, 2006 / Details: MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 8368 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 81.25
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 14.91 / Num. unique all: 812 / Rsym value: 0.232 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GW8

2gw8


Resolution: 1.8→40.52 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 817066.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 451 5.5 %RANDOM
Rwork0.185 ---
obs0.185 8258 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.4117 Å2 / ksol: 0.366011 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms740 0 11 82 833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_mcangle_it2.892
X-RAY DIFFRACTIONc_scbond_it3.52
X-RAY DIFFRACTIONc_scangle_it4.992.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 56 4.3 %
Rwork0.196 1261 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4SO4.PARSO4.TOP

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