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- PDB-5d4l: Structure of the apo form of CPII from Thiomonas intermedia K12, ... -

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Basic information

Entry
Database: PDB / ID: 5d4l
TitleStructure of the apo form of CPII from Thiomonas intermedia K12, a nitrogen regulatory PII-like protein
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
Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesThiomonas intermedia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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


Theoretical massNumber of molelcules
Total (without water)25,9362
Polymers25,9362
Non-polymers00
Water39622
1
A: Nitrogen regulatory protein P-II

A: Nitrogen regulatory protein P-II

A: Nitrogen regulatory protein P-II


Theoretical massNumber of molelcules
Total (without water)38,9043
Polymers38,9043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area5420 Å2
ΔGint-36 kcal/mol
Surface area13540 Å2
MethodPISA
2
B: Nitrogen regulatory protein P-II

B: Nitrogen regulatory protein P-II

B: Nitrogen regulatory protein P-II


Theoretical massNumber of molelcules
Total (without water)38,9043
Polymers38,9043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area4170 Å2
ΔGint-22 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.690, 82.690, 31.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Nitrogen regulatory protein P-II


Mass: 12967.990 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 20% PEG 3500, 0.15 M LD Malic Acid pH 7.0

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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: 2.3→71.61 Å / Num. obs: 10491 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 28.9 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.134 / Χ2: 0.92 / Net I/σ(I): 16.96 / Num. measured all: 121103
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.3610.50.8490.6983.2476668137470.73391.9
2.36-2.420.9090.634.186917877270.65892.4
2.42-2.490.9350.5584.4582627117080.58399.6
2.49-2.570.9390.4855.1885257557390.50797.9
2.57-2.650.9440.4535.881397216800.47394.3
2.65-2.750.9650.3846.5678686746730.40299.9
2.75-2.850.9710.3118.0976176826570.32596.3
2.85-2.970.9790.25910.0272276196080.27198.2
2.97-3.10.9880.20212.5468956056030.21199.7
3.1-3.250.9940.14816.6468495995780.15596.5
3.25-3.420.9950.12320.1564265565560.128100
3.42-3.630.9970.09924.2357125074930.10497.2
3.63-3.880.9980.07630.858615125120.08100
3.88-4.190.9980.06933.1652724634550.07298.3
4.19-4.590.9990.0541.2246324164120.05399
4.59-5.140.9990.04546.3444293823820.047100
5.14-5.930.9990.0636.5638673383350.06399.1
5.93-7.260.9980.0673532222792780.07199.6
7.26-10.270.9990.04349.726532312300.04599.6
10.270.9990.03855.512901191180.0499.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å71.61 Å
Translation3.82 Å71.61 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CZ4

2cz4


Resolution: 2.3→35.806 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 524 5 %
Rwork0.1773 9963 -
obs0.1801 10487 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.02 Å2 / Biso mean: 34.0123 Å2 / Biso min: 16.71 Å2
Refinement stepCycle: final / Resolution: 2.3→35.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 0 22 1496
Biso mean---33.7 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081506
X-RAY DIFFRACTIONf_angle_d1.2282038
X-RAY DIFFRACTIONf_chiral_restr0.052232
X-RAY DIFFRACTIONf_plane_restr0.005263
X-RAY DIFFRACTIONf_dihedral_angle_d15.401538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.52830.29481290.22342443257295
2.5283-2.8940.26791300.22122468259897
2.894-3.64560.27731310.18192500263199
3.6456-35.81020.17931340.14672552268699

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