6V70 | pdb_00006v70

Crystal Structure of Metallo Beta Lactamase from Hirschia baltica with Cadmium in the Active Site

• PDB DOI: https://doi.org/10.2210/pdb6V70/pdb

• Classification: HYDROLASE
• Organism(s): Hirschia baltica ATCC 49814
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-12-06 Released: 2019-12-25 
• Deposition Author(s): Maltseva, N., Kim, Y., Clancy, S., Endres, M., Mulligan, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.183 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Metallo Beta Lactamase from Hirschia baltica.

Maltseva, N., Kim, Y., Clancy, S., Endres, M., Mulligan, R., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.5 kDa 
• Atom Count: 1,823 
• Modeled Residue Count: 217 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	235	Hirschia baltica ATCC 49814	Mutation(s): 1  Gene Names: Hbal_3075 EC: 3.5.2.6
UniProt
Find proteins for C6XID6 (Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418)) Explore C6XID6  Go to UniProtKB:  C6XID6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
EDO	D [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	J [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	B [auth A], C [auth A], E [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.183 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.352	α = 90
b = 80.352	β = 90
c = 245.373	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Maltseva, N., Kim, Y., Clancy, S., Endres, M., Mulligan, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary