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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 Å resolution / Particle / Single particle)
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 Yorodumi Papers
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 19, 2011 / Release: Nov 9, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 9, 2011Structure modelrepositoryInitial release
1.1Nov 30, 2011Structure modelDatabase references
1.2Aug 27, 2014Structure modelOther
1.3Aug 30, 2017Structure modelData collectionem_software_em_software.image_processing_id / _em_software.name

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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)200,10218
Polyers195,6786
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: 32612.963 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: Chemical
ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE


Mass: 310.090 Da / Num. of mol.: 6 / Formula: C5H12O11P2
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: PROTEIN CBBX / Type: COMPLEX
Buffer solutionName: 20 MM TRIS PH 8.0, 50 MM NACL, 5MM MGCL2, 1MM RIBULOSE-1,5- BISPHOSPHATE, 1MM ATP/ATPGAMMAS
Details: 20 MM TRIS PH 8.0, 50 MM NACL, 5MM MGCL2, 1MM RIBULOSE-1,5- BISPHOSPHATE, 1MM ATP/ATPGAMMAS
pH: 8
SpecimenConc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl acetate
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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 90600 / Calibrated magnification: 90600 / Nominal defocus max: 1800 nm / Nominal defocus min: 260 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (2k x 2k)
Image scansNumber digital images: 12
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryImage processing ID
1IMAGICRECONSTRUCTION1
2MRC IMAGE PROCESSING PACKAGERECONSTRUCTION1
3SPIDERRECONSTRUCTION1
CTF correctionDetails: PHASE FLIPPING, EACH PARTICLE
SymmetryPoint symmetry: C6
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 21 Å / Number of particles: 245 / Nominal pixel size: 3.308 / Actual pixel size: 3.308
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.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--RIGID BODY REFINEMENT PROTOCOL--MANUAL / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 3SYL
Least-squares processHighest resolution: 21 Å
Refine hist #LASTHighest resolution: 21 Å
Number of atoms included #LASTProtein: 13614 / Nucleic acid: 0 / Ligand: 270 / Solvent: 0 / Total: 13884

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