4R8U Transferase Dna date Sep 03, 2014
title S-Sad Structure Of Dinb-Dna Complex
authors J.Kottur, D.T.Nair, T.Weinert, V.Oligeric, M.Wang
compound source
Molecule: Dna Polymerase Iv
Chain: A
Fragment: Unp Residues 2-340
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12
Gene: B0231, Dinb, Dinp, Jw0221
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41de3
Expression_system_vector_type: Pgex6p1

Molecule: Dna Polymerase Iv
Chain: B
Fragment: Unp Residues 2-338
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12
Gene: B0231, Dinb, Dinp, Jw0221
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C41de3
Expression_system_vector_type: Pgex6p1

Molecule: Dna
Chain: V, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide

Molecule: Dna
Chain: W
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide

Molecule: Dna
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.181 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.950 57.210 110.600 90.00 94.69 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 1FZ, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceFast native-SAD phasing for routine macromolecular structure determination., Weinert T, Olieric V, Waltersperger S, Panepucci E, Chen L, Zhang H, Zhou D, Rose J, Ebihara A, Kuramitsu S, Li D, Howe N, Schnapp G, Pautsch A, Bargsten K, Prota AE, Surana P, Kottur J, Nair DT, Basilico F, Cecatiello V, Pasqualato S, Boland A, Weichenrieder O, Wang B, Steinmetz MO, Caffrey M, Wang M, Nat Methods. 2014 Dec 15. doi: 10.1038/nmeth.3211. PMID:25506719
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (296 Kb) [Save to disk]
  • Biological Unit Coordinates (4r8u.pdb1.gz) 147 Kb
  • Biological Unit Coordinates (4r8u.pdb2.gz) 144 Kb
  • LPC: Ligand-Protein Contacts for 4R8U
  • CSU: Contacts of Structural Units for 4R8U
  • Structure Factors (717 Kb)
  • Retrieve 4R8U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4R8U from S2C, [Save to disk]
  • Re-refined 4r8u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R8U 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.
  • Visual 3D analysis of 4R8U
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4R8U, from MSDmotif at EBI
  • Fold representative 4r8u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r8u] [4r8u_A] [4r8u_D] [4r8u_C] [4r8u_B] [4r8u_V] [4r8u_W]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4R8U
  • Community annotation for 4R8U at PDBWiki (http://pdbwiki.org)

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