9C3D

Crystal structure of metallo-beta-lactamase superfamily protein CcrA-like_MBL-B1 from Dyadobacter fermentans

PDB DOI: https://doi.org/10.2210/pdb9C3D/pdb

Classification: HYDROLASE
Organism(s): Dyadobacter fermentans DSM 18053
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-31 Released: 2024-07-17
Deposition Author(s): Kim, Y., Maltseva, N., Welk, L., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of metallo-beta-lactamase superfamily protein CcrA-like_MBL-B1 from Dyadobacter fermentans

Kim, Y., Maltseva, N., Welk, L., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Macromolecule Content

Total Structure Weight: 25.02 kDa
Atom Count: 1,898
Modelled Residue Count: 224
Deposited Residue Count: 225
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	225	Dyadobacter fermentans DSM 18053	Mutation(s): 0 Gene Names: Dfer_1371 EC: 3.5.2.6
UniProt
Find proteins for C6W709 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6W709 Go to UniProtKB: C6W709
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6W709
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.176	α = 90
b = 62.256	β = 90
c = 72.387	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-07-17
Type: Initial release

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.