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- PDB-2gw8: Structure of the PII signal transduction protein of Neisseria men... -

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Basic information

Entry
Database: PDB / ID: 2gw8
TitleStructure of the PII signal transduction protein of Neisseria meningitidis at 1.85 resolution
ComponentsPII signal transduction protein
KeywordsSIGNALING PROTEIN / Pii / signal transduction / transcriptional regulation / neisseria / Structural Genomics / Oxford Protein Production Facility / OPPF
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol
Similarity search - Function
Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / 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 P-II, urydylation site / P-II protein uridylation site. / 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
Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNichols, C.E. / Sainsbury, S. / Berrow, N.S. / Alderton, D. / Stammers, D.K. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of the P(II) signal transduction protein of Neisseria meningitidis at 1.85 A resolution.
Authors: Nichols, C.E. / Sainsbury, S. / Berrow, N.S. / Alderton, D. / Saunders, N.J. / Stammers, D.K. / Owens, R.J.
History
DepositionMay 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PII signal transduction protein


Theoretical massNumber of molelcules
Total (without water)12,4841
Polymers12,4841
Non-polymers00
Water2,414134
1
A: PII signal transduction protein

A: PII signal transduction protein

A: PII signal transduction protein


Theoretical massNumber of molelcules
Total (without water)37,4533
Polymers37,4533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6550 Å2
ΔGint-22 kcal/mol
Surface area13640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.141, 61.141, 48.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe asymetric unit contains a monomer, but the known biological oligomeric state is trimeric, with the 3-fold parallel to Z. Two identical biological trimers are thus formed by the application of symetry operations 1-3 and 4-6 respectively. 1. X,Y,Z 2. X-Y,X,1/2+Z 3. -Y,X -Y,Z 4. -X,-Y,1/2+Z 5. -X+Y,-X,Z 6. Y,-X+Y,1/2+Z

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Components

#1: Protein PII signal transduction protein


Mass: 12484.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB1955 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8KUI8, UniProt: Q9JXK6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.17M ammonium sulphate / 25.5% PEG4000 / 15% v/v glycerol, pH Unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2004 / Details: Mirror, vertical focussing
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 8821 / Num. obs: 8803 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 28.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 99.63 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PIL

1pil


Resolution: 1.85→26.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1200787.3 / 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
Rfree0.218 938 10.7 %RANDOM
Rwork0.189 ---
obs0.189 8799 99.7 %-
all-8821 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.4458 Å2 / ksol: 0.370388 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20.25 Å20 Å2
2--1.36 Å20 Å2
3----2.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.85→26.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms757 0 0 134 891
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.963
X-RAY DIFFRACTIONc_mcangle_it4.44
X-RAY DIFFRACTIONc_scbond_it54
X-RAY DIFFRACTIONc_scangle_it7.467
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.323 80 9.5 %
Rwork0.26 766 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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