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- PDB-1ufl: Crystal Structure of TT1020 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1ufl
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 / 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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, H. / Sakai, H. / Hori-Takemoto, C. / Kaminishi, T. / 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
DepositionMay 31, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2003Provider: 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
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_sheet.number_strands
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
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-44 kcal/mol
Surface area14800 Å2
MethodPISA
2
A: Nitrogen regulatory protein P-II
B: Nitrogen regulatory protein P-II
C: Nitrogen regulatory protein P-II

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)77,4066
Polymers77,4066
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area17240 Å2
ΔGint-97 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.070, 97.070, 56.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P83820
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: iso-propanol, PEG4000, Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
20.02 MTris-HCl1drop
30.15 M1droppH8.NaCl
47 %iso-propanol1reservoir
515 %PEG40001reservoir
60.05 Msodium-Hepes1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8743 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 7.7 / % possible all: 92.4
Reflection
*PLUS
Num. measured all: 91310 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 92.4 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.54 Å / Rfactor Rfree error: 0.014 / 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
Rfree0.307 467 5.5 %RANDOM
Rwork0.23 ---
obs-8486 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.239 Å2 / ksol: 0.329293 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.01 Å21.99 Å20 Å2
2--4.01 Å20 Å2
3----8.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 0 35 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 83 6.1 %
Rwork0.33 1269 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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