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- PDB-3l7p: Crystal structure of SMU.1657c, Putative nitrogen regulatory prot... -

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Basic information

Entry
Database: PDB / ID: 3l7p
TitleCrystal structure of SMU.1657c, Putative nitrogen regulatory protein PII from streptococcus mutans
ComponentsPutative nitrogen regulatory protein PII
KeywordsTRANSCRIPTION / nitrogen regulatory protein PII / Streptococcus mutans / SMU_1657c / Transcription regulation
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity
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
Putative nitrogen regulatory protein PII
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFan, X.-X. / Wang, K.-T. / Su, X.-D.
CitationJournal: To be Published
Title: Crystal structure of SMU.1657c, Putative nitrogen regulatory protein PII from streptococcus mutans
Authors: Fan, X.-X. / Wang, K.-T. / Su, X.-D.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative nitrogen regulatory protein PII
B: Putative nitrogen regulatory protein PII
C: Putative nitrogen regulatory protein PII
D: Putative nitrogen regulatory protein PII
E: Putative nitrogen regulatory protein PII
F: Putative nitrogen regulatory protein PII


Theoretical massNumber of molelcules
Total (without water)74,7866
Polymers74,7866
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15470 Å2
ΔGint-95 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.805, 60.805, 147.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Putative nitrogen regulatory protein PII


Mass: 12464.381 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: SMU_1657c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DSV2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.82 Å3/Da / Density % sol: 32.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 3350, 0.1 MES pH6.5, 0.83M NaNO3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.51 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. all: 36010 / Num. obs: 35955 / % possible obs: 99.8 % / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0102refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.9 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.873 / SU B: 6.111 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32661 1792 5 %RANDOM
Rwork0.25805 ---
obs0.26147 34123 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 0 161 4097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223962
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.9875307
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3085511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46326.063127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.78215808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6321513
X-RAY DIFFRACTIONr_chiral_restr0.1340.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022663
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1571.52585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97724178
X-RAY DIFFRACTIONr_scbond_it3.44131377
X-RAY DIFFRACTIONr_scangle_it5.7624.51129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 142 -
Rwork0.264 2500 -
obs--99.92 %

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