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- PDB-1v3r: Crystal structure of TT1020 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1v3r
TitleCrystal structure of TT1020 from Thermus thermophilus HB8
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN / structural genomics / signal transducing protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
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 / 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
Signaling protein / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å
AuthorsWang, H. / Sakai, H. / Takemoto-Hori, C. / Kaminishi, T. / Yamaguchi, H. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8.
Authors: Sakai, H. / Wang, H. / Takemoto-Hori, C. / Kaminishi, T. / Yamaguchi, H. / Kamewari, Y. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionNov 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen regulatory protein P-II
B: Nitrogen regulatory protein P-II
C: Nitrogen regulatory protein P-II


Theoretical massNumber of molelcules
Total (without water)38,7033
Polymers38,7033
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-39 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.520, 75.185, 76.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nitrogen regulatory protein P-II


Mass: 12900.975 Da / Num. of mol.: 3 / Mutation: E18K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET26B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SM86, UniProt: P83820*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: NaCl, sodium acetate, Tris, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 26776 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.283 / Num. unique all: 2621 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.85→19.56 Å / Rfactor Rfree error: 0.006 / 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
Rfree0.225 1263 4.8 %RANDOM
Rwork0.19 ---
obs0.19 26229 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2099 Å2 / ksol: 0.388323 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2---5.45 Å20 Å2
3---7.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 0 178 2333
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_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.791.5
X-RAY DIFFRACTIONc_mcangle_it4.812
X-RAY DIFFRACTIONc_scbond_it6.692
X-RAY DIFFRACTIONc_scangle_it9.432.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 183 4.5 %
Rwork0.209 3891 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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