6B6C

Beta-Lactamase, mixed with Ceftriaxone, needles crystal form, 30ms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.

Olmos, J.L.Pandey, S.Martin-Garcia, J.M.Calvey, G.Katz, A.Knoska, J.Kupitz, C.Hunter, M.S.Liang, M.Oberthuer, D.Yefanov, O.Wiedorn, M.Heyman, M.Holl, M.Pande, K.Barty, A.Miller, M.D.Stern, S.Roy-Chowdhury, S.Coe, J.Nagaratnam, N.Zook, J.Verburgt, J.Norwood, T.Poudyal, I.Xu, D.Koglin, J.Seaberg, M.H.Zhao, Y.Bajt, S.Grant, T.Mariani, V.Nelson, G.Subramanian, G.Bae, E.Fromme, R.Fung, R.Schwander, P.Frank, M.White, T.A.Weierstall, U.Zatsepin, N.Spence, J.Fromme, P.Chapman, H.N.Pollack, L.Tremblay, L.Ourmazd, A.Phillips, G.N.Schmidt, M.

(2018) BMC Biol 16: 59-59

  • DOI: https://doi.org/10.1186/s12915-018-0524-5
  • Primary Citation of Related Structures:  
    6B5X, 6B5Y, 6B68, 6B69, 6B6A, 6B6B, 6B6C, 6B6D, 6B6E, 6B6F

  • PubMed Abstract: 

    Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases.


  • Organizational Affiliation

    Department of BioSciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase267Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: blaCblaARv2068cMTCY49.07c
EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKD3 
Go to UniProtKB:  P9WKD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKD3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9F2 (Subject of Investigation/LOI)
Query on 9F2

Download Ideal Coordinates CCD File 
B [auth A]Ceftriaxone
C18 H18 N8 O7 S3
VAAUVRVFOQPIGI-TYHRLYECSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.53α = 90
b = 41.59β = 104.81
c = 69.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references