7M5F | pdb_00007m5f

Contact-dependent inhibition system from Serratia marcescens BWH57

PDB DOI: https://doi.org/10.2210/pdb7M5F/pdb

Classification: TOXIN
Organism(s): Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-23 Released: 2021-05-12
Deposition Author(s): Michalska, K., Nutt, W., Stols, L., Jedrzejczak, R., Hayes, C.S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.167 (Depositor), 0.169 (DCC)
R-Value Work:
0.140 (Depositor), 0.143 (DCC)
R-Value Observed:
0.142 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7M5F

This is version 1.2 of the entry. See complete history.

Literature

Contact-dependent inhibition system from Serratia marcescens

Michalska, K., Nutt, W., Stols, L., Jedrzejczak, R., Hayes, C.S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 27.25 kDa
Atom Count: 2,135
Modeled Residue Count: 217
Deposited Residue Count: 241
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdiI	A	98	Serratia marcescens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin CdiA	B [auth C]	143	Serratia marcescens	Mutation(s): 0 Gene Names: SK68_03206
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth C] SDF format, chain E [auth C] MOL2 format, chain C [auth A] MOL2 format, chain D [auth C] MOL2 format, chain E [auth C] mmCIF format, chain C [auth A] mmCIF format, chain D [auth C] mmCIF format, chain E [auth C]	C [auth A], D [auth C], E [auth C]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth C] Focus chain E [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth C] Focus chain E [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.167 (Depositor), 0.169 (DCC)
R-Value Work: 0.140 (Depositor), 0.143 (DCC)
R-Value Observed: 0.142 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.691	α = 90
b = 97.241	β = 90
c = 44.495	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Jedrzejczak, R.

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2021-08-18
Changes: Database references, Structure summary
Version 1.2: 2024-10-23
Changes: Data collection, Structure summary

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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.