2PLS | pdb_00002pls

Structural Genomics, the crystal structure of the CorC/HlyC transporter associated domain of a CBS domain protein from Chlorobium tepidum TLS

PDB DOI: https://doi.org/10.2210/pdb2PLS/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Chlorobaculum tepidum TLS
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2007-04-20 Released: 2007-05-22
Deposition Author(s): Tan, K., Volkart, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The crystal structure of the CorC/HlyC transporter associated domain of a CBS domain protein from Chlorobium tepidum TLS.

Tan, K., Volkart, L., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 120.83 kDa
Atom Count: 8,932
Modeled Residue Count: 1,027
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	86	Chlorobaculum tepidum TLS	Mutation(s): 3 Gene Names: CT0541
UniProt
Find proteins for Q8KEZ1 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KEZ1 Go to UniProtKB: Q8KEZ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KEZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain IA [auth I] SDF format, chain MA [auth J] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain IA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain IA [auth I] mmCIF format, chain MA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	AA [auth F] BA [auth F] CA [auth F] IA [auth I] MA [auth J] AA [auth F], BA [auth F], CA [auth F], IA [auth I], MA [auth J], N [auth A], O [auth A], P [auth B], R [auth C], S [auth C], T [auth C], Y [auth E], Z [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain IA [auth I] Focus chain MA [auth J] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain IA [auth I] Focus chain MA [auth J] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth E] Focus chain Z [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain NA [auth K] SDF format, chain V [auth D] SDF format, chain X [auth E] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth K] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth K] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E]	M [auth A], NA [auth K], V [auth D], X [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain NA [auth K] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain M [auth A] Focus chain NA [auth K] Focus chain V [auth D] Focus chain X [auth E]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain KA [auth I] SDF format, chain OA [auth L] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain JA [auth I] MOL2 format, chain KA [auth I] MOL2 format, chain OA [auth L] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain JA [auth I] mmCIF format, chain KA [auth I] mmCIF format, chain OA [auth L] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain JA [auth I]	JA [auth I] KA [auth I] OA [auth L] Q [auth B] U [auth C] JA [auth I], KA [auth I], OA [auth L], Q [auth B], U [auth C], W [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain JA [auth I] Focus chain KA [auth I] Focus chain OA [auth L] Focus chain Q [auth B] Focus chain U [auth C] Focus chain W [auth D] Interactions & Density Focus chain JA [auth I] Focus chain KA [auth I] Focus chain OA [auth L] Focus chain Q [auth B] Focus chain U [auth C] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain LA [auth J] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain LA [auth J] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth I] mmCIF format, chain LA [auth J]	DA [auth G] EA [auth H] FA [auth H] GA [auth I] HA [auth I] DA [auth G], EA [auth H], FA [auth H], GA [auth I], HA [auth I], LA [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain LA [auth J] Interactions & Density Focus chain DA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain LA [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.243	α = 90
b = 108.493	β = 90
c = 106.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-05-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary