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- PDB-4c3m: Structure of wildtype PII from S. elongatus at medium resolution -

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Basic information

Entry
Database: PDB / ID: 4c3m
TitleStructure of wildtype PII from S. elongatus at medium resolution
ComponentsNITROGEN REGULATORY PROTEIN P-II
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding / identical protein binding
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
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsZeth, K. / Forchhammer, K.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis and Target-Specific Modulation of Adp Sensing by the Synechococcus Elongatus Pii Signaling Protein.
Authors: Zeth, K. / Fokina, O. / Forchhammer, K.
History
DepositionAug 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)37,2283
Polymers37,2283
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-26.3 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.418, 73.418, 95.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:36 OR RESSEQ 55:108 )
211CHAIN B AND (RESSEQ 1:36 OR RESSEQ 55:107 )
311CHAIN C AND (RESSEQ 1:36 OR RESSEQ 55:108 )

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Components

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


Mass: 12409.347 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3F4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.8 Å3/Da / Density % sol: 33 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM HEPES, 20% PEG8000, PH 7.5

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Data collection

DiffractionMean temperature: 100 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: 2.15→95 Å / Num. obs: 16722 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AFF

4aff


Resolution: 2.149→63.582 Å / SU ML: 0.3 / σ(F): 2.02 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 836 5 %
Rwork0.2098 --
obs0.2111 16721 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.149→63.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 0 60 2123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082073
X-RAY DIFFRACTIONf_angle_d1.1462782
X-RAY DIFFRACTIONf_dihedral_angle_d16.032794
X-RAY DIFFRACTIONf_chiral_restr0.075351
X-RAY DIFFRACTIONf_plane_restr0.006348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A676X-RAY DIFFRACTIONPOSITIONAL
12B676X-RAY DIFFRACTIONPOSITIONAL0.034
13C688X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1489-2.28360.34771360.27562594X-RAY DIFFRACTION100
2.2836-2.45990.31291380.27282612X-RAY DIFFRACTION100
2.4599-2.70750.30781370.24652610X-RAY DIFFRACTION100
2.7075-3.09920.24241370.24482629X-RAY DIFFRACTION100
3.0992-3.90460.23641400.21322659X-RAY DIFFRACTION100
3.9046-63.60970.19781480.17722781X-RAY DIFFRACTION100
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)
18.03112.1289-2.94983.61920.38627.1011-1.02291.39060.4028-1.04740.7755-0.0792-0.6538-0.6205-0.0070.6493-0.2622-0.08660.59850.01620.2996-21.901229.3022-4.8848
22.3243-1.35131.27958.16341.51318.93890.19870.8548-0.4542-0.98910.04340.1376-0.29180.2659-0.32790.4394-0.2276-0.05390.4885-0.03150.4357-16.101327.95970.1019
31.70571.4559-0.28123.65310.95715.6827-0.48181.2162-0.6969-0.83160.37850.13940.017-0.29520.07790.432-0.1803-0.03610.6398-0.12990.3648-23.821523.7372-3.5783
43.53583.8412-1.24824.6866-0.36542.5507-0.40010.44650.99910.44220.13022.70330.0126-0.8933-0.09430.3489-0.02650.15990.5126-0.07750.745-30.588736.122414.9002
52.23980.2904-0.36314.9699-0.49441.71760.4113-1.0410.21091.0923-0.256-0.0785-0.19580.733-0.09740.5343-0.21360.05760.5736-0.07930.3014-16.319735.849719.2498
65.4281-2.1805-2.77310.86741.09372.26990.1995-1.2439-0.08991.48950.18750.5179-1.4128-0.1652-0.72380.9938-0.34530.16890.88910.05210.2601-14.23529.328125.5367
75.15913.25420.17335.534-16.1833-0.72310.98530.5333-0.81770.48910.8008-0.74730.2131-1.1428-0.161-0.49370.15830.50090.11650.3746-14.157934.85066.0798
86.81840.9994-1.97194.4733-0.17144.0480.4486-0.62050.58480.5349-0.24150.1135-0.47030.1055-0.30750.368-0.16340.10460.404-0.0790.2556-22.054935.027717.58
96.6229-1.0622-0.34811.36350.4720.16240.2343-2.878-2.03841.7234-0.072-0.05080.477-0.2116-0.30490.7817-0.1559-0.23820.74080.46360.783-14.092113.664922.5868
102.88191.7669-0.00422.94830.172.52720.0771-0.0726-1.2298-0.11920.1221-0.85580.52650.4697-0.20990.50610.0659-0.12210.3863-0.12610.8612-7.760613.49949.8895
111.97140.2108-1.13152.4438-2.49065.80730.40880.7646-1.47650.7031-0.1957-0.99411.9127-0.0449-0.89750.86710.0825-0.27560.6838-0.26790.9175-12.15549.42192.7891
126.77184.41264.49693.56183.60153.62470.5314-0.36040.55670.20180.4884-1.0096-0.02650.5151-0.35850.3273-0.06360.07360.5735-0.0590.5547-7.347826.690112.1892
130.5903-0.75-0.40181.7368-0.6252.01040.05520.0427-1.98480.04960.2482-1.01050.85210.2677-0.05830.52420.0251-0.10270.32790.03511.0698-12.601212.3111.9053
143.1662-1.7205-0.51642.31350.24610.0884-0.2667-0.7135-0.98990.8308-0.0558-1.23590.78890.7067-0.27690.7745-0.0035-0.35240.72880.37961.0284-2.255715.317522.7638
152.0026-2.20060.71083.0497-1.90593.06010.5263-0.6182-1.58420.3924-0.2334-0.61760.3750.523-0.24740.3151-0.0512-0.05690.37380.16040.6012-18.097916.937116.0827
164.68561.2669-1.61452.4478-2.72063.3743-0.09850.9149-1.284-0.99870.1202-0.44831.0592-0.05390.16770.5963-0.19470.05160.6524-0.23340.6676-25.592414.9951-4.0016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 22 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 23 THROUGH 55 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 56 THROUGH 95 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 96 THROUGH 109 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1 THROUGH 22 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 23 THROUGH 28 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 29 THROUGH 55 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 56 THROUGH 95 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 96 THROUGH 107 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 1 THROUGH 22 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 23 THROUGH 28 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 29 THROUGH 55 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 56 THROUGH 81 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 82 THROUGH 89 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 90 THROUGH 95 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 96 THROUGH 108 )

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