6JLG

Crystal Structure of HasAp with Co-9,10,19,20-Tetraphenylporphycene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Highly malleable haem-binding site of the haemoprotein HasA permits stable accommodation of bulky tetraphenylporphycenes.

Sakakibara, E.Shisaka, Y.Onoda, H.Koga, D.Xu, N.Ono, T.Hisaeda, Y.Sugimoto, H.Shiro, Y.Watanabe, Y.Shoji, O.

(2019) RSC Adv 9: 18697-18702


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heme acquisition protein HasA
A, B, C, D, E
A, B, C, D, E, F, G, H
184Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
UniProt
Find proteins for G3XD33 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD33 
Go to UniProtKB:  G3XD33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XD33
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BWU
Query on BWU

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
P [auth D]
R [auth E]
I [auth A],
L [auth B],
O [auth C],
P [auth D],
R [auth E],
U [auth F],
V [auth G],
Z [auth H]
Tetraphenylporphycene contating cobalt
C44 H28 Co N4
PWICVPBSZDUOSZ-LIDSSYNJSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
S [auth E],
W [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth H]
J [auth A]
K [auth A]
M [auth B]
N [auth B]
AA [auth H],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
Q [auth D],
T [auth E],
X [auth G],
Y [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 237.58α = 90
b = 92.221β = 100.96
c = 93.195γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18H02084

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description