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- PDB-2xbp: A novel signal transduction protein PII variant from Synechococcu... -

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Basic information

Entry
Database: PDB / ID: 2xbp
TitleA novel signal transduction protein PII variant from Synechococcus elongatus PCC7942 indicates a two-step process for NAGK PII complex formation
ComponentsNITROGEN REGULATORY PROTEIN P-II
KeywordsGENE REGULATION / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTION / PHOSPHOPROTEIN
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / identical protein 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
ADENOSINE-5'-TRIPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFokina, O. / Chellamuthu, V.R. / Zeth, K. / Forchhammer, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A Novel Signal Transduction Protein P(II) Variant from Synechococcus Elongatus Pcc 7942 Indicates a Two-Step Process for Nagk- P(II) Complex Formation.
Authors: Fokina, O. / Chellamuthu, V.R. / Zeth, K. / Forchhammer, K.
History
DepositionApr 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0644
Polymers12,4971
Non-polymers5673
Water3,135174
1
A: NITROGEN REGULATORY PROTEIN P-II
hetero molecules

A: NITROGEN REGULATORY PROTEIN P-II
hetero molecules

A: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,19312
Polymers37,4923
Non-polymers1,7019
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
Buried area10120 Å2
ΔGint-39.6 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.682, 80.682, 80.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1116-

CL

21A-2058-

HOH

31A-2100-

HOH

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Components

#1: Protein NITROGEN REGULATORY PROTEIN P-II / PII SIGNAL TRANSDUCING PROTEIN


Mass: 12497.370 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PII FROM FROM SYNECHOCOCCUS ELONGATUS PCC7942 / Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3F4
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 86 TO ASN

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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: 2.78 Å3/Da / Density % sol: 55.35 % / Description: NONE
Crystal growpH: 7 / Details: PH 7

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 54696 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 14 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.04
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 11 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→36.08 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.752 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.144 2741 5 %RANDOM
Rwork0.125 ---
obs0.126 52061 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.74 Å2
Refinement stepCycle: LAST / Resolution: 1.2→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 33 174 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.022967
X-RAY DIFFRACTIONr_bond_other_d0.0050.02672
X-RAY DIFFRACTIONr_angle_refined_deg2.7342.0181318
X-RAY DIFFRACTIONr_angle_other_deg1.3131658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88724.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82615193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.566158
X-RAY DIFFRACTIONr_chiral_restr0.2090.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02184
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_it2.5721.5580
X-RAY DIFFRACTIONr_mcbond_other0.9071.5241
X-RAY DIFFRACTIONr_mcangle_it3.832952
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.2113387
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.9544.5358
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.55531639
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 200 -
Rwork0.202 3786 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.162-0.0605-0.34132.584-0.71081.00430.0076-0.0297-0.0001-0.0545-0.0290.02980.04380.07920.02140.03010.00330.01780.01590.00040.038229.385-12.76861.152
20.1676-0.3108-0.15240.60640.20630.42210.0036-0.06310.0376-0.02450.0899-0.04810.00280.1464-0.09350.01380.0007-0.00110.0518-0.03080.029938.4550.16260.005
30.5278-0.3361-0.00981.09090.05370.4942-0.00910.04580.0091-0.0875-0.0471-0.0016-0.1264-0.06440.05620.05310.0139-0.01150.0133-0.00450.024123.44810.84950.275
40.2832-0.56560.51382.7304-1.47411.06150.01760.02290.01060.0106-0.02270.04980.00670.04740.00510.0264-0.00140.00940.03380.00230.023933.598-4.77756.12
50.26230.6793-0.26137.44650.94310.72260.0175-0.0296-0.02080.3738-0.042-0.0990.09830.03370.02450.0582-0.0013-0.01640.0159-0.00120.017431.635-8.5670.013
60.0869-0.0501-0.06220.22120.10860.1050.0017-0.0396-0.00580.0072-0.01060.028-0.00220.02990.00890.01990.00020.00220.0305-0.00220.025132.23-8.71860.779
75.31210.9271.03850.6948-1.54285.78420.0622-0.2593-0.00850.0594-0.107-0.0132-0.13120.15780.04480.03910.01910.02310.04230.02160.017638.778-22.65864.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 33
3X-RAY DIFFRACTION3A34 - 56
4X-RAY DIFFRACTION4A57 - 65
5X-RAY DIFFRACTION5A66 - 77
6X-RAY DIFFRACTION6A78 - 106
7X-RAY DIFFRACTION7A107 - 113

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