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- PDB-2xul: Structure of PII from Synechococcus elongatus in complex with 2- ... -

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Basic information

Entry
Database: PDB / ID: 2xul
TitleStructure of PII from Synechococcus elongatus in complex with 2- oxoglutarate at high 2-OG concentrations
ComponentsNITROGEN REGULATORY PROTEIN P-II
KeywordsSIGNALING PROTEIN / GLNK
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
2-OXOGLUTARIC ACID / ADENOSINE-5'-TRIPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZeth, K. / Chellamuthu, V.-R. / Forchhammer, K. / Fokina, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism of 2-Oxoglutarate Signaling by the Synechococcus Elongatus Pii Signal Transduction Protein
Authors: Fokina, O. / Chellamuthu, V.-R. / Forchhammer, K. / Zeth, K.
History
DepositionOct 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 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 / Refinement description
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_ncs_dom_lim / struct_sheet / 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.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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
D: NITROGEN REGULATORY PROTEIN P-II
E: NITROGEN REGULATORY PROTEIN P-II
F: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58824
Polymers76,5226
Non-polymers4,06618
Water4,450247
1
A: NITROGEN REGULATORY PROTEIN P-II
B: NITROGEN REGULATORY PROTEIN P-II
C: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,29412
Polymers38,2613
Non-polymers2,0339
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-48 kcal/mol
Surface area15830 Å2
MethodPISA
2
D: NITROGEN REGULATORY PROTEIN P-II
E: NITROGEN REGULATORY PROTEIN P-II
F: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,29412
Polymers38,2613
Non-polymers2,0339
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-43.1 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.870, 87.987, 116.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 3 - 110 / Label seq-ID: 3 - 110

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

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


Mass: 12753.712 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: WITH C-TERMINAL STREP TAG / Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PASK-IBA3 (IBA) / 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.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.4 Å3/Da / Density % sol: 48.78 % / Description: NONE
Crystal growpH: 7.4 / Details: pH 7.4

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→29 Å / Num. obs: 36239 / % possible obs: 99.6 % / Observed criterion σ(I): 2.6 / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 2.6
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.09 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.663 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22488 1908 5 %RANDOM
Rwork0.17929 ---
obs0.18161 36239 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: 27.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2--0.5 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 252 247 5417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0225207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0412.0297029
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76425200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53515976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6781536
X-RAY DIFFRACTIONr_chiral_restr0.1350.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023646
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8651.53178
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64625139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.11332029
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1484.51889
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 756 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.340.5
2Bmedium positional0.490.5
3Cmedium positional0.390.5
4Dmedium positional0.330.5
5Emedium positional0.420.5
6Fmedium positional0.380.5
1Amedium thermal1.252
2Bmedium thermal1.422
3Cmedium thermal1.342
4Dmedium thermal1.42
5Emedium thermal1.42
6Fmedium thermal1.162
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 133 -
Rwork0.221 2522 -
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)
10.5303-0.22450.37051.7293-0.24660.793-0.0484-0.1727-0.01470.13990.01980.0675-0.0401-0.16960.02850.02820.01330.00410.077-0.00670.00820.8777-18.471820.9731
20.7695-0.48070.22680.8016-0.36210.79-0.0495-0.12950.03430.12750.032-0.0317-0.0358-0.07710.01750.02910.0078-0.01050.0539-0.01340.00955.5636-17.876320.2134
319.82723.07011.790717.1668-9.06497.57860.1265-0.44990.36230.4803-0.15840.2322-0.98550.20630.03180.2661-0.0597-0.04650.0644-0.0730.15494.8254-0.014310.576
41.34630.71190.87660.38550.36962.189-0.0710.0371-0.1058-0.04450.0125-0.07240.09830.04420.05840.0190.00920.00920.0371-0.0160.059312.5838-31.95727.6816
51.0965-0.2220.23630.7864-0.33691.33540.01930.0326-0.1471-0.07230.0020.01150.1267-0.0833-0.02130.0149-0.00780.00070.0109-0.01040.029912.4884-30.25484.4897
60.59760.21860.24030.78560.3811.3643-0.0445-0.03410.00480.04310.05-0.1017-0.13380.0372-0.00560.02680.0105-0.01210.0337-0.0020.019115.4064-24.70317.2845
70.5163-0.24250.15350.64290.10350.82370.00120.06210.0074-0.0265-0.0434-0.01120.0104-0.06020.04220.01020.0153-0.00510.0518-0.00770.0220.8536-14.89670.1214
80.6682-0.36140.04930.68250.13020.214-0.01590.06010.0785-0.0352-0.0325-0.0416-0.0811-0.03810.04840.03210.0097-0.0190.0636-0.00440.024.5375-13.18882.9679
98.569-9.622111.885714.5729-23.978746.5280.03410.58460.38180.33280.1341-0.1577-0.9789-1.1582-0.16820.2124-0.13410.03760.37620.04090.265420.7264-20.6655-4.7637
101.61310.1506-0.36720.03970.14391.3637-0.0757-0.0144-0.0276-0.0297-0.00620.0015-0.1407-0.0340.08190.0638-0.0052-0.0010.01080.01330.047926.285234.67267.6444
110.8685-0.3540.44170.69750.00420.60250.02030.0290.0385-0.0159-0.0176-0.058-0.09280.0652-0.00270.0325-0.01660.00330.02790.02390.035626.913230.08984.2261
120.8035-0.18940.63710.3359-0.17750.5799-0.0415-0.15870.00190.02880.04950.06330.0278-0.0913-0.0080.06480.02090.00670.08160.01060.024524.291626.466715.9832
130.676-0.32440.12380.2312-0.03750.25530.00820.0475-0.029-0.0183-0.03350.05160.0889-0.02470.02520.0446-0.0221-0.00210.04460.00250.031640.191414.29564.684
141.179-0.50290.40210.2829-0.08440.24960.04660.0496-0.20480.0171-0.00770.11130.0560.0371-0.03890.0568-0.0275-0.00510.04640.01290.057431.043913.59621.4356
1513.3147-8.7038-3.68615.82314.815545.20160.69931.8188-1.1296-0.3084-1.13490.73542.5224-0.21430.43560.3761-0.0137-0.05630.376-0.0710.251618.517519.9911-3.857
160.7371-0.11440.34451.2874-0.68781.0469-0.1287-0.11870.07330.09570.0786-0.0485-0.06730.06080.05010.05580.0031-0.02180.0932-0.00250.017736.97925.885521.7338
170.6278-0.3358-0.09230.4660.22560.735-0.0258-0.1579-0.09080.04950.04810.02740.0518-0.0354-0.02230.0555-0.01630.00040.06110.03810.029934.195618.405420.9082
184.3385-2.97627.11067.7815-5.124711.74350.2736-0.1468-0.25730.4520.03180.7180.5695-0.2101-0.30530.28140.00660.22370.02270.08320.462735.64111.228512.4494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 38
2X-RAY DIFFRACTION2A39 - 106
3X-RAY DIFFRACTION3A107 - 113
4X-RAY DIFFRACTION4B1 - 16
5X-RAY DIFFRACTION5B17 - 82
6X-RAY DIFFRACTION6B83 - 113
7X-RAY DIFFRACTION7C1 - 39
8X-RAY DIFFRACTION8C40 - 107
9X-RAY DIFFRACTION9C108 - 113
10X-RAY DIFFRACTION10D1 - 21
11X-RAY DIFFRACTION11D22 - 82
12X-RAY DIFFRACTION12D83 - 113
13X-RAY DIFFRACTION13E1 - 69
14X-RAY DIFFRACTION14E70 - 103
15X-RAY DIFFRACTION15E104 - 109
16X-RAY DIFFRACTION16F1 - 53
17X-RAY DIFFRACTION17F54 - 104
18X-RAY DIFFRACTION18F105 - 113

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