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- PDB-5d4o: Structure of CPII, a nitrogen regulatory PII-like protein from Th... -

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Basic information

Entry
Database: PDB / ID: 5d4o
TitleStructure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound to ADP, AMP and bicarbonate.
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN / carbon regulatory PII protein / CPII / nitrogen regulatory PII protein / nucleotide binding / ADP hydrolysis / bicarbonate binding / acetate binding
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding
Similarity search - Function
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'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / BICARBONATE ION / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesThiomonas intermedia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionAug 8, 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 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)36,7497
Polymers35,8533
Non-polymers8964
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-24 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.440, 75.450, 80.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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) / Strain (production host): BL21(DE3) / References: UniProt: D5X329
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.15 M KBr, 30% (w/v) PEG MME 2000

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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
ReflectionHighest resolution: 1.8 Å / Num. obs: 29590 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.42 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.055 / Χ2: 1.033 / Net I/σ(I): 19.24 / Num. measured all: 191688
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
1.8-1.840.840.5632.7411606216420370.61894.1
1.84-1.890.9280.4144.314329211021080.44999.9
1.89-1.950.9560.3335.4213756204020350.36199.8
1.95-2.010.9750.2467.1513409200720060.267100
2.01-2.070.9820.2058.5513044196219600.22399.9
2.07-2.150.9840.16610.2311893185418510.18199.8
2.15-2.230.990.13312.2411321183418320.14599.9
2.23-2.320.9940.1214.812001173917350.1399.8
2.32-2.420.9940.0991711531168816870.10799.9
2.42-2.540.9960.08519.4910864160916070.09399.9
2.54-2.680.9970.07621.5410050153215270.08399.7
2.68-2.840.9970.06125.328783146414580.06799.6
2.84-3.030.9970.05430.859378138913860.05999.8
3.03-3.280.9980.04536.248488128212760.04999.5
3.28-3.590.9990.03840.937525117911740.04199.6
3.59-4.010.9990.03642.576473108810830.03999.5
4.01-4.630.9990.03146.0957979629560.03399.4
4.63-5.680.9990.02948.1752988338330.032100
5.68-8.030.9990.02943.8538326536470.03299.1
8.030.9990.02450.9223103933920.02799.7

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.0refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D4L

5d4l


Resolution: 1.8→54.9 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.9328 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 1503 5.1 %RANDOM
Rwork0.2059 ---
obs0.2072 29486 99.74 %-
Displacement parametersBiso max: 117.69 Å2 / Biso mean: 35.69 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.6196 Å20 Å20 Å2
2--0.3755 Å20 Å2
3---2.2441 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: final / Resolution: 1.8→54.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 84 100 2477
Biso mean--25.17 37.06 -
Num. residues----300
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d851SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes388HARMONIC5
X-RAY DIFFRACTIONt_it2444HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion305SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2735SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2444HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3328HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion17.55
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2389 132 4.61 %
Rwork0.2244 2731 -
all0.2251 2863 -
obs--99.74 %
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)
11.3429-0.0818-0.12431.65110.62241.55920.03060.10420.1006-0.26250.0088-0.1256-0.1601-0.003-0.0394-0.0228-0.00730.0233-0.04950.0133-0.06419.7433-17.5239-28.8359
21.1821.1310.27133.39240.74231.77110.0787-0.19440.12880.4641-0.10060.09150.0034-0.02170.022-0.0418-0.01330.0072-0.02910.0021-0.083815.9917-15.7523-9.8956
31.34080.0464-0.02522.29160.31713.652-0.0343-0.0647-0.16860.19310.0070.37210.416-0.31460.0273-0.0648-0.04210.0209-0.06640.0153-0.06037.177-29.5849-19.482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 108
2X-RAY DIFFRACTION2{ B|* }B5 - 104
3X-RAY DIFFRACTION3{ C|* }C4 - 107

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