2R8D | pdb_00002r8d

The structure of transporter associated domain CorC_HlyC from a Xylella fastidiosa Temecula1 hemolysin in complex with Mg++ and Mn++

PDB DOI: https://doi.org/10.2210/pdb2R8D/pdb

Classification: TOXIN
Organism(s): Xylella fastidiosa Temecula1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-09-10 Released: 2007-11-13
Deposition Author(s): Cuff, M.E., Volkart, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.220 (Depositor), 0.227 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The structure of transporter associated domain CorC in complex with Mg++ and Mn++ from Xylella fastidiosa.

Cuff, M.E., Volkart, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 10.83 kDa
Atom Count: 712
Modeled Residue Count: 79
Deposited Residue Count: 94
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin	A	94	Xylella fastidiosa Temecula1	Mutation(s): 0 Gene Names: tlyC
UniProt
Find proteins for Q87DZ3 (Xylella fastidiosa (strain Temecula1 / ATCC 700964)) Explore Q87DZ3 Go to UniProtKB: Q87DZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87DZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.220 (Depositor), 0.227 (DCC)
R-Value Work: 0.171 (Depositor), 0.172 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.061	α = 90
b = 88.061	β = 90
c = 88.061	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2025-03-26
Changes: Data collection, Database references, Derived calculations, 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.