5HD8 | pdb_00005hd8

Crystal structure of disulfide cross-linked D417C ClC-ec1

• PDB DOI: https://doi.org/10.2210/pdb5HD8/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12, Mus musculus
• Expression System: Escherichia coli BL21(DE3), Mus musculus
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2016-01-05 Released: 2017-01-18 
• Deposition Author(s): Mathews, I.I., Khantwal, C.M., Maduke, M.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.257 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Conformational change in CLC transporters: beyond the rotation of Gluex

Khantwal, C.M., Abraham, S.J., Han, W., Jiang, T., Chavan, T.S., Cheng, R.C., Elvington, S.M., Liu, C.W., Mathews, I.I., Stein, R.A., Mchaourab, H.S., Tajkhorshid, E., Maduke, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Macromolecule Content 

• Total Structure Weight: 190.03 kDa 
• Atom Count: 13,068 
• Modeled Residue Count: 1,728 
• Deposited Residue Count: 1,766 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)/Cl(-) exchange transporter ClcA	A, B	450	Escherichia coli K-12	Mutation(s): 1  Gene Names: clcA, eriC, yadQ, b0155, JW5012 Membrane Entity: Yes
UniProt
Find proteins for P37019 (Escherichia coli (strain K12)) Explore P37019  Go to UniProtKB:  P37019

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB FRAGMENT (HEAVY CHAIN)	C, E	222	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB FRAGMENT (LIGHT CHAIN)	D, F	211	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth A], H [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.257 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.74	α = 90
b = 96.06	β = 131.58
c = 169.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Mathews, I.I., Khantwal, C.M., Maduke, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1021472
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM087519
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM086749
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	P41-RR05969

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary