7K8E | pdb_00007k8e

Beta-lactamase mixed with Ceftriaxone, 5ms

PDB DOI: https://doi.org/10.2210/pdb7K8E/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-26 Released: 2021-09-22
Deposition Author(s): Pandey, S., Schmidt, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.250 (Depositor), 0.251 (DCC)
R-Value Work:
0.234 (Depositor), 0.235 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Pandey, S., Calvey, G., Katz, A.M., Malla, T.N., Koua, F.H.M., Martin-Garcia, J.M., Poudyal, I., Yang, J.H., Vakili, M., Yefanov, O., Zielinski, K.A., Bajt, S., Awel, S., Doerner, K., Frank, M., Gelisio, L., Jernigan, R., Kirkwood, H., Kloos, M., Koliyadu, J., Mariani, V., Miller, M.D., Mills, G., Nelson, G., Olmos, J.L.J., Sadri, A., Sato, T., Tolstikova, A., Xu, W., Ourmazd, A., Spence, J.C.H., Schwander, P., Barty, A., Chapman, H.N., Fromme, P., Mancuso, A.P., Phillips, G.N.J., Bean, R., Pollack, L., Schmidt, M.

(2021) IUCrJ 8: 878-895

DOI: https://doi.org/10.1107/S2052252521008125

Macromolecule Content

Total Structure Weight: 115.09 kDa
Atom Count: 8,290
Modeled Residue Count: 1,060
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	267	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: blaC, ERS027646_02769 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WKD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9F2 (Subject of Investigation/LOI) Query on 9F2 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth D] MOL2 format, chain F [auth B] MOL2 format, chain I [auth D] mmCIF format, chain F [auth B] mmCIF format, chain I [auth D]	F [auth B], I [auth D]	Ceftriaxone C₁₈ H₁₈ N₈ O₇ S₃ VAAUVRVFOQPIGI-TYHRLYECSA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth C], J [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.250 (Depositor), 0.251 (DCC)
R-Value Work: 0.234 (Depositor), 0.235 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.68	α = 90
b = 98.78	β = 108.6
c = 113.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data scaling
PDB_EXTRACT	data extraction
CrystFEL	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release
Version 1.1: 2021-11-10
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.