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- PDB-1hwu: STRUCTURE OF PII PROTEIN FROM HERBASPIRILLUM SEROPEDICAE -

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Basic information

Entry
Database: PDB / ID: 1hwu
TitleSTRUCTURE OF PII PROTEIN FROM HERBASPIRILLUM SEROPEDICAE
ComponentsPII PROTEIN
KeywordsSIGNALING PROTEIN / Herbaspirillum seropedicae PII / Beta-alpha-beta motif / signal transduction protein
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 / 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 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 / 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 P-II protein
Similarity search - Component
Biological speciesHerbaspirillum seropedicae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBenelli, E.M. / Buck, M. / Polikarpov, I. / De Souza, E.M. / Cruz, L.M. / Pedrosa, F.O.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Herbaspirillum seropedicae signal transduction protein PII is structurally similar to the enteric GlnK.
Authors: Machado Benelli, E. / Buck, M. / Polikarpov, I. / Maltempi de Souza, E. / Cruz, L.M. / Pedrosa, F.O.
History
DepositionJan 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: PII PROTEIN
B: PII PROTEIN
C: PII PROTEIN
D: PII PROTEIN
E: PII PROTEIN
F: PII PROTEIN


Theoretical massNumber of molelcules
Total (without water)73,7056
Polymers73,7056
Non-polymers00
Water2,126118
1
A: PII PROTEIN
B: PII PROTEIN
C: PII PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,8533
Polymers36,8533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-25 kcal/mol
Surface area14150 Å2
MethodPISA
2
D: PII PROTEIN
E: PII PROTEIN
F: PII PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,8533
Polymers36,8533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-19 kcal/mol
Surface area13560 Å2
MethodPISA
3
A: PII PROTEIN
B: PII PROTEIN
C: PII PROTEIN

D: PII PROTEIN
E: PII PROTEIN
F: PII PROTEIN


Theoretical massNumber of molelcules
Total (without water)73,7056
Polymers73,7056
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area13730 Å2
ΔGint-50 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.410, 82.320, 100.950
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
PII PROTEIN


Mass: 12284.189 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum seropedicae (bacteria) / Gene: GLNB / Plasmid: PET28B+ / Production host: Escherichia coli (E. coli) / Strain (production host): RB9065(LAMBDA)DE3 / References: UniProt: P94852
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Cacodylate, Magnesium Acetate, Methylpentadiol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
350 mM1dropNaCl
420 %glycerol1drop
50.1 mMEDTA1drop
630 %MPD1reservoir
70.1 mMsodium cacodylate1reservoirpH6.5
80.2 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.1→13 Å / Num. all: 146413 / Num. obs: 36523 / % possible obs: 94.4 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.322 / Num. unique all: 36523 / % possible all: 95.5
Reflection
*PLUS
% possible obs: 94 % / Redundancy: 3 %
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 95 % / Num. unique obs: 2415

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PII

2pii


Resolution: 2.1→13 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.272 5 RANDOM
Rwork0.203 --
all-146413 -
obs-146413 -
Refinement stepCycle: LAST / Resolution: 2.1→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 0 118 4431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_d0.044
X-RAY DIFFRACTIONo_angle_deg
Refinement
*PLUS
Num. reflection obs: 36331 / Num. reflection Rfree: 1820 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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