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- PDB-5c3c: Structural characterization of a newly identified component of al... -

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Basic information

Entry
Database: PDB / ID: 5c3c
TitleStructural characterization of a newly identified component of alpha-carboxysomes: The AAA+ domain Protein cso-CbbQ
ComponentsCbbQ/NirQ/NorQ domain protein
KeywordsPROTEIN BINDING / ATPase / AAA+ domain protein / carboxysome-associated
Function / homologyCbbQ/NirQ/NorQ, C-terminal / CbbQ/NirQ/NorQ C-terminal / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ADENOSINE-5'-DIPHOSPHATE / CbbQ/NirQ/NorQ domain protein
Function and homology information
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSutter, M. / Kerfeld, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-91ER20021 United States
CitationJournal: Sci Rep / Year: 2015
Title: Structural Characterization of a Newly Identified Component of alpha-Carboxysomes: The AAA+ Domain Protein CsoCbbQ.
Authors: Sutter, M. / Roberts, E.W. / Gonzalez, R.C. / Bates, C. / Dawoud, S. / Landry, K. / Cannon, G.C. / Heinhorst, S. / Kerfeld, C.A.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CbbQ/NirQ/NorQ domain protein
B: CbbQ/NirQ/NorQ domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3454
Polymers63,4902
Non-polymers8542
Water0
1
A: CbbQ/NirQ/NorQ domain protein
B: CbbQ/NirQ/NorQ domain protein
hetero molecules

A: CbbQ/NirQ/NorQ domain protein
B: CbbQ/NirQ/NorQ domain protein
hetero molecules

A: CbbQ/NirQ/NorQ domain protein
B: CbbQ/NirQ/NorQ domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,03512
Polymers190,4716
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-y+3,x-y,z1
crystal symmetry operation3_885-x+y+3,-x+3,z1
Buried area22420 Å2
ΔGint-58 kcal/mol
Surface area53630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.913, 171.913, 53.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CbbQ/NirQ/NorQ domain protein


Mass: 31745.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Strain: ATCC 23641 / c2 / Gene: Hneap_0905 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D0KZ75
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mg/ml protein, 0.1 M HEPES, 8 % ethylene glycol, 6% PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2014
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.8→38.8 Å / Num. obs: 14510 / % possible obs: 99.88 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1126 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.314 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→38.798 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 35.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1451 10.01 %Random selection
Rwork0.2256 ---
obs0.2313 14501 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→38.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 54 0 3709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043772
X-RAY DIFFRACTIONf_angle_d0.95113
X-RAY DIFFRACTIONf_dihedral_angle_d15.4491431
X-RAY DIFFRACTIONf_chiral_restr0.031587
X-RAY DIFFRACTIONf_plane_restr0.004653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.41091470.28351313X-RAY DIFFRACTION100
2.9001-3.01610.36781460.28951290X-RAY DIFFRACTION100
3.0161-3.15330.32231430.27131325X-RAY DIFFRACTION100
3.1533-3.31950.35841440.27331300X-RAY DIFFRACTION100
3.3195-3.52740.3171470.26671296X-RAY DIFFRACTION100
3.5274-3.79950.3261420.241307X-RAY DIFFRACTION100
3.7995-4.18150.23311450.21331316X-RAY DIFFRACTION100
4.1815-4.78560.26391470.18961303X-RAY DIFFRACTION100
4.7856-6.02570.27761460.22541301X-RAY DIFFRACTION100
6.0257-38.80150.23771440.19421299X-RAY DIFFRACTION99

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