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- PDB-3zuh: Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco... -

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Basic information

Entry
Database: PDB / ID: 3zuh
TitleNegative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides
DescriptorPROTEIN CBBX
KeywordsATP BINDING PROTEIN / AAA+ PROTEIN
Specimen sourceRhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス
MethodElectron microscopy (21 A resolution / Single particle / Negative stain)
AuthorsMueller-Cajar, O. / Stotz, M. / Wendler, P. / Hartl, F.U. / Bracher, A. / Hayer-Hartl, M.
CitationNature, 2011, 479, 194-199

Nature, 2011, 479, 194-199 StrPapers
Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
Oliver Mueller-Cajar / Mathias Stotz / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl

DateDeposition: Jul 19, 2011 / Release: Nov 9, 2011 / Last modification: Aug 27, 2014

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Assembly

Deposited unit
A: PROTEIN CBBX
B: PROTEIN CBBX
C: PROTEIN CBBX
D: PROTEIN CBBX
E: PROTEIN CBBX
F: PROTEIN CBBX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,10318
Polyers195,6796
Non-polymers4,42412
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)
PROTEIN CBBX / RUBISCO ACTIVASE CBBX


Mass: 32613.229 Da / Num. of mol.: 6 / Details: THE PROTEIN IS BOUND TO RIBULOSE-1,5-BISPHOSPHATE
Source: (gene. exp.) Rhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス
References: UniProt: P95648

Molecular function

#2: Sugar
ChemComp-RUB / SUGAR (RIBULOSE-1,5-DIPHOSPHATE)


Mass: 310.091 Da / Num. of mol.: 6 / Formula: C5H12O11P2
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.203 Da / Num. of mol.: 6 / Formula: C10H15N5O10P2
Nonpolymer detailsADENOSINE-5'-DIPHOSPHATE (ADP): MODELLED FROM P97 D2 (PDB 3CF3)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: NEGATIVE STAIN

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Sample preparation

Assembly of specimenName: PROTEIN CBBX / Aggregation state: PARTICLE
Buffer solutionName: 20 MM TRIS PH 8.0, 50 MM NACL, 5MM MGCL2, 1MM RIBULOSE-1,5- BISPHOSPHATE, 1MM ATP/ATPGAMMAS
Sample preparationpH: 8 / Sample conc.: 0.07 mg/ml
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 12 / Date: Nov 19, 2010
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Illumination mode: LOW DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 90600 X / Calibrated magnification: 90600 X / Nominal defocus max: 1800 nm / Nominal defocus min: 260 nm / Cs: 2 mm
CameraType: EAGLE 2K CCD
EM image scansNumber digital images: 12
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: MRC, IMAGIC, SPIDER / Number of particles: 245
EM single particle entitySymmetry type: MIXED SYMMETRY
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 21 A / Nominal pixel size: 3.308 A/pix / Actual pixel size: 3.308 A/pix / CTF correction method: PHASE FLIPPING, EACH PARTICLE
Details: MODULE CONSISTING OF CHAIN A (204-296) AND CHAIN B (8-203) AS FOUND IN PDB 3SYL WAS MODELLED ONTO D2 P97 OF PDB 3CF3. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1932.
Atomic model buildingMethod: RIGID BODY / Ref protocol: MANUAL / Ref space: REAL
Atomic model buildingPDB-ID: 3SYL
Least-squares processHighest resolution: 21 A
Refine hist #LASTHighest resolution: 21 A
Number of atoms included #LASTProtein: 13614 / Nucleic acid: 0 / Ligand: 270 / Solvent: 0 / Total: 13884

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