3A9L Hydrolase date Oct 30, 2009
title Structure Of Bacteriophage Poly-Gamma-Glutamate Hydrolase
authors Z.Fujimoto, K.Kimura
compound source
Molecule: Poly-Gamma-Glutamate Hydrolase
Chain: A, B
Engineered: Yes
Organism_scientific: Bacillus Phage Phinit1
Organism_taxid: 207656
Gene: Pghp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnag443
symmetry Space Group: P 32
R_factor 0.281 R_Free 0.315
length a length b length c angle alpha angle beta angle gamma
86.809 86.809 85.116 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand PO4, ZN enzyme
A, B

Primary referenceCrystal structure of bacteriophage varphiNIT1 zinc peptidase PghP that hydrolyzes gamma-glutamyl linkage of bacterial poly-gamma-glutamate., Fujimoto Z, Kimura K, Proteins. 2012 Mar;80(3):722-32. doi: 10.1002/prot.23229. Epub 2011 Nov 22. PMID:22105902
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (3a9l.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 3A9L
  • CSU: Contacts of Structural Units for 3A9L
  • Structure Factors (815 Kb)
  • Retrieve 3A9L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A9L from S2C, [Save to disk]
  • Re-refined 3a9l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A9L in 3D
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  • Visual 3D analysis of 3A9L
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  • 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 3A9L, from MSDmotif at EBI
  • Fold representative 3a9l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a9l] [3a9l_A] [3a9l_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3A9L
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  • MMDB (Entrez's Structure Database)
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