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- PDB-4aff: High resolution structure of a PII mutant (I86N) protein in compl... -

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Basic information

Entry
Database: PDB / ID: 4aff
TitleHigh resolution structure of a PII mutant (I86N) protein in complex with ATP, MG and FLC
ComponentsNITROGEN REGULATORY PROTEIN P-II
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding / 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / CITRATE ANION / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsZeth, K. / Fokina, O. / Chellamuthu, V.R. / Forchhammer, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: An Engineered Pii Protein Variant that Senses a Novel Ligand: Atomic Resolution Structure of the Complex with Citrate.
Authors: Zeth, K. / Fokina, O. / Forchhammer, K.
History
DepositionJan 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references / Structure summary
Revision 1.2Aug 15, 2012Group: Database references
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 / 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 / _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.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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,5624
Polymers12,8421
Non-polymers7213
Water2,342130
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)40,68712
Polymers38,5253
Non-polymers2,1629
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area12300 Å2
ΔGint-68.7 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.087, 62.087, 51.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2106-

HOH

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Components

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


Mass: 12841.734 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Plasmid: IBA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A3F5, UniProt: P0A3F4*PLUS
#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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.81 Å3/Da / Density % sol: 31.65 % / Description: NONE
Crystal growpH: 5.6 / Details: pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / 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: 1.05→37 Å / Num. obs: 49584 / % possible obs: 99.6 % / Observed criterion σ(I): 2.1 / Redundancy: 7.2 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→137 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.621 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 -7 %RANDOM
Rwork0.12 ---
obs0.13 49582 99 %-
Solvent computationSolvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.05→137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 45 130 1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0221012
X-RAY DIFFRACTIONr_bond_other_d0.0040.02700
X-RAY DIFFRACTIONr_angle_refined_deg2.4282.0241387
X-RAY DIFFRACTIONr_angle_other_deg1.25931739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42725.23842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7115203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.422157
X-RAY DIFFRACTIONr_chiral_restr0.150.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021110
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02187
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_it0.0050.02187
X-RAY DIFFRACTIONr_mcbond_other0.8331.5249
X-RAY DIFFRACTIONr_mcangle_it3.2382995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9133408
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.794.5379
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
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.25 3566 -
obs--98 %
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)
12.0142-0.5774-2.65880.59740.70963.24750.04480.01070.04230.00360.0215-0.01140.0131-0.0182-0.06630.02310.0044-0.00550.06-0.00060.03112.4526.77225.533
21.8434-0.3016-1.40480.73990.13641.8388-0.16130.1813-0.16760.00180.05150.06120.2156-0.13950.10980.0544-0.0159-0.00050.0368-0.01330.0489-1.78917.15719.266
31.49640.5035-1.07560.1444-0.35330.94550.03010.08370.0242-0.0020.0441-0.0049-0.0478-0.1086-0.07420.02460.01430.00450.0545-0.00170.03433.7330.41717.104
41.8550.7718-1.41980.9782-0.59041.7241-0.0063-0.09840.0204-0.11210.0531-0.0635-0.08420.0806-0.04680.04540.00320.01770.0492-0.0140.044712.3333.08212.755
51.0153-0.2178-0.77990.23330.16880.7345-0.06220.016-0.03550.03170.02470.00240.1149-0.0140.03750.03430.0040.00370.0431-0.00060.02953.32222.30327.7
60.9062-0.21260.44970.7059-0.02741.6736-0.0199-0.0353-0.02110.01020.02150.03630.0335-0.1069-0.00160.0162-0.01480.00820.04890.010.0338-16.8729.13530.532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 27
3X-RAY DIFFRACTION3A28 - 37
4X-RAY DIFFRACTION4A51 - 60
5X-RAY DIFFRACTION5A61 - 97
6X-RAY DIFFRACTION6A98 - 114

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