PDB-3zuh: NEGATIVE STAIN EM MAP OF THE AAA PROTEIN CBBX, A RED-TY...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3zuh
Title	NEGATIVE STAIN EM MAP OF THE AAA PROTEIN CBBX, A RED-TYPE RUBISCO ACTIVASE FROM R. SPHAEROIDES
Descriptor	PROTEIN CBBX
Keywords	ATP BINDING PROTEIN, AAA+ PROTEIN
Authors	Mueller-Cajar, O., Stotz, M., Wendler, P., Hartl, F.U., Bracher, A., Hayer-Hartl, M.
Date	Deposition: 2011-07-19, Release: 2011-11-09
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Nonpolymer details	ADENOSINE-5'-DIPHOSPHATE (ADP): MODELLED FROM P97 D2 (PDB 3CF3)
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1932, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1932 CiteFit PDB-3syk Cite PDB-3syl Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-1218 EMDB-2181 PDB-1mhs PDB-3zw6 List of similar structure data about Omokage system

Article
Citation - primary
Article	Nature, Vol. 479, Issue 7372, Page 194-9, Year 2011
Title	Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
Authors	Oliver Mueller-Cajar, Mathias Stotz, Petra Wendler, F Ulrich Hartl, Andreas Bracher, Manajit Hayer-Hartl Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
Keywords	Adenosine Triphosphate (metabolism, 56-65-5), Allosteric Regulation (drug effects), Bacterial Proteins (chemistry), Carbon Dioxide (metabolism, 124-38-9), CbbX protein, Rhodobacter sphaeroides, Crystallography, X-Ray, Enzyme Activation (drug effects), Models, Molecular, Protein Multimerization (drug effects), Protein Structure, Quaternary (drug effects), Rhodobacter sphaeroides (enzymology), Ribulose-Bisphosphate Carboxylase (metabolism, 4.1.1.39), Ribulosephosphates (metabolism), Structure-Activity Relationship, ribulose-1,5 diphosphate (2002-28-0)
Links	DOI: 10.1038/nature10568, PubMed: 22048315

Components
ID 1 : RUBISCO ACTIVASE CBBX
Image
Description	PROTEIN CBBX
Type	polymer
Formula weight	32613.229 Da
Number of molecules	6
Details	THE PROTEIN IS BOUND TO RIBULOSE-1,5-BISPHOSPHATE
Source	Method: Isolated from a genetically manipulated source Gene: ID:1063, RHODOBACTER SPHAEROIDES Host: ID:469008, ESCHERICHIA COLI , BL21(DE3), PHUE, PLASMID
Links	UniProt: P95648, Sequence view
ID 2 : SUGAR (RIBULOSE-1,5-DIPHOSPHATE)
Image
Description	SUGAR (RIBULOSE-1,5-DIPHOSPHATE)
Type	non-polymer
Formula weight	310.091 Da
Number of molecules	6
Source	Method: Isolated from a genetically manipulated source
ID 3 : ADENOSINE-5'-DIPHOSPHATE
Image
Description	ADENOSINE-5'-DIPHOSPHATE
Type	non-polymer
Formula weight	427.203 Da
Number of molecules	6
Source	Method: Obtained synthetically

Sample
Assembly
Aggregation state	PARTICLE
Name	PROTEIN CBBX
Buffer
Name	20 MM TRIS PH 8.0, 50 MM NACL, 5MM MGCL2, 1MM RIBULOSE-1,5- BISPHOSPHATE, 1MM ATP/ATPGAMMAS
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	NEGATIVE STAIN
Sample preparation
pH	8.0
Sample concentration	0.07 mg/ml
Sample support
Details	CARBON

Processing
2D projection selection
Number of particles	245
Software name	MRC, IMAGIC, SPIDER
Single particle entity
Symmetry type	MIXED SYMMETRY
3D reconstruction
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.
Method	ANGULAR RECONSTITUTION
Nominal pixel size	3.308 A/pix
Resolution	21 A
3D fitting
Method	RIGID BODY
Refinement Protocol	MANUAL
Refinement Space	REAL
3D fitting list
PDB entry ID	3SYL PDB-3syl
Refine
Ls d res high	21.00 A
ID	1
Refine hist
D res high	21.00
Total atoms	13884
Ligand atoms	270
Protein atoms	13614