OCA Atlas for 2B3G

2B3G

Replication

date

Sep 20, 2005

title

P53n (Fragment 33-60) Bound To Rpa70n

authors

E.Bochkareva, L.Kaustov, A.Ayed, G.S.Yi, Y.Lu, A.Pineda-Lucena, J.C.Liao, A.L.Okorokov, J.Milner, C.H.Arrowsmith, A.Bochkarev

compound

source

Molecule: Replication Protein A 70 Kda Dna-Binding Subunit
Chain: A
Fragment: N-Terminal Domain (Residues 1-120)
Synonym: Rp-A, Rf-A, Replication Factor-A Protein 1, Single-Stranded Dna-Binding Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rpa1, Repa1, Rpa70
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b-Rpa70n-P53n

Molecule: Cellular Tumor Antigen P53
Chain: B
Fragment: Residues 33-60
Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen Ny-Co-13;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tp53, P53
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b-Rpa70n-P53n

symmetry

Space Group: P 21 21 21

R_factor

0.204

R_Free

0.239

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
49.460	50.380	52.320	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

1.60 Å

Primary reference

Single-stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A., Bochkareva E, Kaustov L, Ayed A, Yi GS, Lu Y, Pineda-Lucena A, Liao JC, Okorokov AL, Milner J, Arrowsmith CH, Bochkarev A, Proc Natl Acad Sci U S A 2005 Oct 25;102(43):15412-7. Epub 2005 Oct 17. PMID:16234232

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]

Biological Unit Coordinates (2b3g.pdb1.gz) 74 Kb

CSU: Contacts of Structural Units for 2B3G

Likely Quarternary Molecular Structure file(s) for 2B3G

Structure Factors (118 Kb)

Retrieve 2B3G in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2B3G from S2C, [Save to disk]

Re-refined 2b3g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2B3G in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2B3G

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

3D motif for 2B3G, from MSDmotif at EBI

Fold representative 2b3g from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2b3g_A] [2b3g_B]

SWISS-PROT database: [P04637] [P27694]

Domain organization of [P53_HUMAN] [RFA1_HUMAN] by SWISSPFAM

Alignments of the sequence of 2B3G with the sequences similar proteins can be viewed for 2B3G's classification [P53_HUMAN] [RFA1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.

A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [P53_HUMAN] [RFA1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2B3G

Community annotation for 2B3G at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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