2P4P | pdb_00002p4p

Crystal structure of a CorC_HlyC domain from Haemophilus ducreyi

• PDB DOI: https://doi.org/10.2210/pdb2P4P/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): [Haemophilus] ducreyi 35000HP
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-03-12 Released: 2007-05-22 
• Deposition Author(s): Cuff, M.E., Volkart, L., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.262 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

The structure of a CorC_HlyC domain from Haemophilus ducreyi

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 21.76 kDa 
• Atom Count: 1,527 
• Modelled Residue Count: 161 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein HD1797	A, B	86	[Haemophilus] ducreyi 35000HP	Mutation(s): 12  Gene Names: TlyC, HD_1797
UniProt
Find proteins for Q7VKS4 (Haemophilus ducreyi (strain 35000HP / ATCC 700724)) Explore Q7VKS4  Go to UniProtKB:  Q7VKS4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.262 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.552	α = 90
b = 58.667	β = 90
c = 87.434	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
autoSHARP	phasing
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Cuff, M.E., Volkart, L., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• 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, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary