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- PDB-5drk: 2.3 Angstrom Structure of CPII, a nitrogen regulatory PII-like pr... -

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Basic information

Entry
Database: PDB / ID: 5drk
Title2.3 Angstrom Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound to ADP, AMP and bicarbonate.
ComponentsNitrogen regulatory protein P-II
KeywordsMETAL BINDING 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 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'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / BICARBONATE ION / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesThiomonas intermedia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 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 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / 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)36,6886
Polymers35,8533
Non-polymers8353
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-29 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.510, 75.610, 79.860
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
1ILEILEGLYGLYchain AAA4 - 1014 - 101
2ALAALAARGARGchain BBB3 - 1073 - 107
3LYSLYSPHEPHEchain CCC5 - 1065 - 106

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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.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: 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
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 43.29 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.2
Details: 0.2 M Sodium dihydrogen Phosphate monohydrate, 20% w/v PEG 3350

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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: 2.38→54.91 Å / Num. obs: 13864 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 37.41 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.118 / Χ2: 0.917 / Net I/σ(I): 20.51 / Num. measured all: 160664
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
2.38-2.440.7950.9463.06103579479100.9996.1
2.44-2.510.8790.8123.78114499229220.847100
2.51-2.580.9180.6964.42111869009000.726100
2.58-2.660.9440.565.57107558598590.584100
2.66-2.740.9560.4726.39107328628620.493100
2.74-2.840.9750.3897.72102978258250.406100
2.84-2.950.990.27910.2699027947940.291100
2.95-3.070.9910.22912.2297017777770.238100
3.07-3.210.9940.1716.591777327310.17799.9
3.21-3.360.9960.13619.6588827107100.142100
3.36-3.540.9980.125.5783706686680.105100
3.54-3.760.9980.07831.8280656466460.081100
3.76-4.020.9990.0734.1976006146140.073100
4.02-4.340.9990.05741.9771165715710.059100
4.34-4.750.9990.04251.7764075235230.044100
4.75-5.3210.04549.4458344774770.047100
5.32-6.140.9990.05540.9952674354350.058100
6.14-7.520.9990.05640.8443983703700.058100
7.52-10.6310.03162.4133642962960.033100
10.6310.02869.4618051891870.02998.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.33 Å75.61 Å
Translation2.33 Å75.61 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: 2.38→54.91 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 694 5.01 %
Rwork0.2439 13168 -
obs0.2439 13862 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.45 Å2 / Biso mean: 44.7192 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.38→54.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 78 7 2204
Biso mean--24.03 37.22 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182229
X-RAY DIFFRACTIONf_angle_d1.7233020
X-RAY DIFFRACTIONf_chiral_restr0.112347
X-RAY DIFFRACTIONf_plane_restr0.005374
X-RAY DIFFRACTIONf_dihedral_angle_d18.451791
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1199X-RAY DIFFRACTION16.682TORSIONAL
12B1199X-RAY DIFFRACTION16.682TORSIONAL
13C1199X-RAY DIFFRACTION16.682TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3275-2.50690.32681340.30882537267198
2.5069-2.75920.37431370.29926052742100
2.7592-3.15840.26791380.282426152753100
3.1584-3.97910.23451390.242826502789100
3.9791-54.92060.19621460.202227612907100
Refinement TLS params.Method: refined / Origin x: 66.3391 Å / Origin y: 20.5858 Å / Origin z: 21.0329 Å
111213212223313233
T0.2398 Å2-0.005 Å20.0186 Å2-0.2661 Å20.0255 Å2--0.2322 Å2
L2.0136 °2-0.4742 °20.4414 °2-3.0138 °21.1788 °2--3.3486 °2
S0.0274 Å °0.0699 Å °-0.0028 Å °-0.0419 Å °-0.0641 Å °0.0566 Å °-0.0362 Å °-0.0872 Å °0.0153 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 101
2X-RAY DIFFRACTION1allB3 - 107
3X-RAY DIFFRACTION1allC5 - 106
4X-RAY DIFFRACTION1allD2
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF2 - 4
7X-RAY DIFFRACTION1allF7
8X-RAY DIFFRACTION1allF8 - 10
9X-RAY DIFFRACTION1allG1

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