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- PDB-5ds7: 2.0 A Structure of CPII, a nitrogen regulatory PII-like protein f... -

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Basic information

Entry
Database: PDB / ID: 5ds7
Title2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound AMP
ComponentsNitrogen regulatory protein P-II
KeywordsMETAL BINDING PROTEIN / carbon regulatory PII protein / CPII / nitrogen regulatory PII protein / nucleotide binding / ADP hydrolysis / bicarbonate / acetate binding
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding
Similarity search - Function
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 MONOPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesThiomonas intermedia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWheatley, N.M. / Ngo, J. / Cascio, D. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein.
Authors: Wheatley, N.M. / Eden, K.D. / Ngo, J. / Rosinski, J.S. / Sawaya, M.R. / Cascio, D. / Collazo, M. / Hoveida, H. / Hubbell, W.L. / Yeates, T.O.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9307
Polymers35,8533
Non-polymers1,0774
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-40 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.870, 75.650, 80.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ILEILEPROPROchain AAA4 - 1034 - 103
2ALAALAARGARGchain BBB3 - 1073 - 107
3ILEILEARGARGchain CCC4 - 1074 - 107

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Components

#1: Protein Nitrogen regulatory protein P-II


Mass: 11950.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiomonas intermedia (strain K12) (bacteria)
Strain: K12 / Gene: Tint_0114 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5X329
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 273 K / Method: evaporation / Details: 0.1 M Citric acid pH 4.0, 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→43.566 Å / Num. obs: 21369 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 27.53 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.094 / Χ2: 0.938 / Net I/σ(I): 22.79 / Num. measured all: 304488
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.8380.8493.4719322158814740.88292.8
2.05-2.110.9060.7074.3722270158115370.73297.2
2.11-2.170.9390.5735.3321641152914890.59497.4
2.17-2.230.9680.6085.1718261145212600.6386.8
2.23-2.310.980.23113.2718419144112720.23988.3
2.31-2.390.9810.3418.7719953140813720.35397.4
2.39-2.480.9880.26111.1219259134713250.2798.4
2.48-2.580.9890.2312.6818356128112640.23998.7
2.58-2.690.9940.18715.2617822124612260.19498.4
2.69-2.830.9960.14519.1417077118511710.1598.8
2.83-2.980.9970.11823.0916660115711490.12299.3
2.98-3.160.9980.08530.2915413107810680.08899.1
3.16-3.380.9990.0736.7714648102210180.07399.6
3.38-3.650.9990.05544.63133629519390.05798.7
3.65-40.9990.04652.78124458928770.04898.3
4-4.470.9990.0458.36111437997940.04299.4
4.47-5.1610.03364.7100187227220.034100
5.16-6.320.9990.04155.7984736206200.043100
6.32-8.9310.03756.3865104934930.039100
8.9310.03167.0234363052990.03298

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.93 Å80.27 Å
Translation5.93 Å80.27 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.566 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1068 5.01 %
Rwork0.2305 20262 -
obs0.2318 21330 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 33.7955 Å2 / Biso min: 16.49 Å2
Refinement stepCycle: final / Resolution: 2→43.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 70 63 2323
Biso mean--29.14 37.48 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132323
X-RAY DIFFRACTIONf_angle_d1.6543152
X-RAY DIFFRACTIONf_chiral_restr0.088357
X-RAY DIFFRACTIONf_plane_restr0.007389
X-RAY DIFFRACTIONf_dihedral_angle_d16.782831
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1226X-RAY DIFFRACTION13.971TORSIONAL
12B1226X-RAY DIFFRACTION13.971TORSIONAL
13C1226X-RAY DIFFRACTION13.971TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.08880.31521280.27442429255795
2.0888-2.19890.31521310.28222495262697
2.1989-2.33670.39591190.38842256237587
2.3367-2.51710.26581340.25552539267398
2.5171-2.77030.27111350.25622566270199
2.7703-3.17110.28991370.24652591272899
3.1711-3.99480.21541380.20512627276599
3.9948-43.5760.20721460.176427592905100
Refinement TLS params.Method: refined / Origin x: -11.2046 Å / Origin y: 16.7522 Å / Origin z: -20.8392 Å
111213212223313233
T0.1568 Å2-0.0135 Å2-0.0024 Å2-0.1834 Å20.0192 Å2--0.1317 Å2
L1.6216 °20.1196 °2-0.0262 °2-2.7569 °20.6927 °2--2.2703 °2
S0.0404 Å °-0.0682 Å °-0.0168 Å °0.1054 Å °-0.0455 Å °0.0776 Å °0.1202 Å °-0.1077 Å °-0.0071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 103
2X-RAY DIFFRACTION1allB3 - 107
3X-RAY DIFFRACTION1allC4 - 107
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allD3
6X-RAY DIFFRACTION1allE2 - 68
7X-RAY DIFFRACTION1allF1

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