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- PDB-5d4n: Structure of CPII bound to ADP, AMP and acetate, from Thiomonas i... -

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Basic information

Entry
Database: PDB / ID: 5d4n
TitleStructure of CPII bound to ADP, AMP and acetate, from Thiomonas intermedia K12
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
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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesThiomonas intermedia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
Model detailsnitrogen regulatory PII superfamily protein
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)36,7457
Polymers35,8533
Non-polymers8934
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-31 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.530, 75.410, 79.550
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 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5X329
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.9
Details: 0.1 M acetate pH 4.6, 30% PEG 2000, 0.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→54.73 Å / Num. obs: 41577 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.01 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.041 / Χ2: 1.082 / Net I/σ(I): 21.38 / Num. measured all: 267556
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.640.7020.8521.9119026306229840.92797.5
1.64-1.680.8340.6482.6820034295929550.70299.9
1.68-1.730.9120.4773.5919178288028790.517100
1.73-1.790.9480.3584.7918670282728270.388100
1.79-1.850.9690.2656.2617172271027060.28899.9
1.85-1.910.980.2068.7615908263426120.22599.2
1.91-1.980.9870.15712.1516926257725510.1799
1.98-2.060.9940.10715.8716635244724440.11599.9
2.06-2.160.9950.08619.6715880236723660.093100
2.16-2.260.9960.07622.8413775224422230.08399.1
2.26-2.380.9980.05726.1212960215021450.06299.8
2.38-2.530.9980.0531.6413518204120410.054100
2.53-2.70.9990.04436.3613096193919380.04899.9
2.7-2.920.9990.03841.9811792179117890.04299.9
2.92-3.20.9990.03346.5910295166416600.03699.8
3.2-3.570.9990.02949.088396151315050.03299.5
3.57-4.130.9990.02756.788485134913460.02999.8
4.13-5.050.9990.02359.447242115711530.02599.7
5.05-7.150.9990.02154.752169169090.02399.2
7.150.9990.02259.7733525445440.024100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å54.73 Å
Translation1.6 Å54.73 Å

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.0refinement
XSCALEdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D4L

5d4l


Resolution: 1.6→54.73 Å / Cor.coef. Fo:Fc: 0.9492 / Cor.coef. Fo:Fc free: 0.9364 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 2095 5.05 %RANDOM
Rwork0.2115 ---
obs0.2127 41508 99.69 %-
Displacement parametersBiso max: 111.71 Å2 / Biso mean: 35.51 Å2 / Biso min: 17.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.194 Å20 Å20 Å2
2---0.6952 Å20 Å2
3---2.8892 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: final / Resolution: 1.6→54.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 58 103 2376
Biso mean--24.96 38.37 -
Num. residues----293
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d816SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes372HARMONIC5
X-RAY DIFFRACTIONt_it2354HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion302SEMIHARMONIC5
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_contact2739SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2354HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3193HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion15.44
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2291 151 4.99 %
Rwork0.2408 2875 -
all0.2402 3026 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: -11.0277 Å / Origin y: 16.8396 Å / Origin z: -20.7775 Å
111213212223313233
T-0.1058 Å2-0.0115 Å2-0.0037 Å2--0.084 Å20.0158 Å2---0.0811 Å2
L1.017 °20.0927 °2-0.1181 °2-2.2799 °20.6414 °2--1.7369 °2
S0.0296 Å °-0.0595 Å °-0.0022 Å °0.005 Å °-0.0469 Å °0.063 Å °0.0638 Å °-0.0807 Å °0.0173 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A3 - 107
2X-RAY DIFFRACTION1{ *|* }B4 - 103
3X-RAY DIFFRACTION1{ *|* }C4 - 108
4X-RAY DIFFRACTION1{ *|* }D1 - 2
5X-RAY DIFFRACTION1{ *|* }E1 - 104
6X-RAY DIFFRACTION1{ *|* }F1 - 2

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