6SJJ

A new modulated crystal structure of ANS complex of St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A new modulated crystal structure of the ANS complex of the St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell.

Smietanska, J.Sliwiak, J.Gilski, M.Dauter, Z.Strzalka, R.Wolny, J.Jaskolski, M.

(2020) Acta Crystallogr D Struct Biol 76: 653-667

  • DOI: https://doi.org/10.1107/S2059798320006841
  • Primary Citation of Related Structures:  
    6SJJ

  • PubMed Abstract: 

    Superstructure modulation, with violation of the strict short-range periodic order of consecutive crystal unit cells, is well known in small-molecule crystallography but is rarely reported for macromolecular crystals. To date, one modulated macromolecular crystal structure has been successfully determined and refined for a pathogenesis-related class 10 protein from Hypericum perforatum (Hyp-1) crystallized as a complex with 8-anilinonaphthalene-1-sulfonate (ANS) [Sliwiak et al. (2015), Acta Cryst. D71, 829-843]. The commensurate modulation in that case was interpreted in a supercell with sevenfold expansion along c. When crystallized in the additional presence of melatonin, the Hyp-1-ANS complex formed crystals with a different pattern of structure modulation, in which the supercell shows a ninefold expansion of c, manifested in the diffraction pattern by a wave of reflection-intensity modulation with crests at l = 9n and l = 9n ± 4. Despite complicated tetartohedral twinning, the structure has been successfully determined and refined to 2.3 Å resolution using a description in a ninefold-expanded supercell, with 36 independent Hyp-1 chains and 156 ANS ligands populating the three internal (95 ligands) and five interstitial (61 ligands) binding sites. The commensurate superstructures and ligand-binding sites of the two crystal structures are compared, with a discussion of the effect of melatonin on the co-crystallization process.


  • Organizational Affiliation

    Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Krakow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PR-10 protein163Hypericum perforatumMutation(s): 0 
Gene Names: PR10.1
UniProt
Find proteins for A0A160HRF0 (Hypericum perforatum)
Explore A0A160HRF0 
Go to UniProtKB:  A0A160HRF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A160HRF0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2AN (Subject of Investigation/LOI)
Query on 2AN

Download Ideal Coordinates CCD File 
AB [auth Q]
AC [auth K]
AD [auth F]
AE [auth d]
AF [auth Z]
AB [auth Q],
AC [auth K],
AD [auth F],
AE [auth d],
AF [auth Z],
AG [auth U],
AH [auth h],
BB [auth Q],
BC [auth K],
BD [auth F],
BE [auth d],
BF [auth Z],
BG [auth U],
BH [auth h],
CB [auth Q],
CC [auth J],
CD [auth F],
CE [auth d],
CF [auth Z],
CG [auth T],
CH [auth g],
DC [auth J],
DD [auth F],
DE [auth d],
DF [auth Z],
DG [auth T],
DH [auth g],
EB [auth P],
EC [auth J],
ED [auth F],
EE [auth c],
EF [auth Z],
EG [auth T],
EH [auth g],
FB [auth P],
FC [auth I],
FD [auth F],
FE [auth c],
FF [auth Y],
FG [auth T],
GB [auth P],
GC [auth I],
GD [auth E],
GE [auth c],
GF [auth Y],
GG [auth T],
HB [auth P],
HC [auth I],
HD [auth E],
HE [auth c],
HF [auth Y],
HG [auth S],
IC [auth I],
ID [auth E],
IE [auth c],
IF [auth Y],
IG [auth S],
JB [auth O],
JC [auth I],
JD [auth E],
JE [auth c],
JG [auth S],
KA [auth B],
KB [auth O],
KC [auth I],
KF [auth X],
KG [auth S],
LA [auth B],
LB [auth O],
LC [auth I],
LD [auth D],
LF [auth X],
LG [auth j],
MA [auth B],
MB [auth N],
MD [auth D],
MF [auth X],
MG [auth j],
NA [auth B],
NB [auth N],
NC [auth H],
ND [auth D],
NE [auth b],
NF [auth X],
NG [auth j],
OA [auth B],
OB [auth N],
OC [auth H],
OD [auth D],
OE [auth b],
OF [auth X],
OG [auth j],
PA [auth B],
PB [auth N],
PC [auth H],
PD [auth C],
PE [auth b],
PF [auth X],
PG [auth j],
QA [auth A],
QB [auth N],
QC [auth H],
QD [auth C],
QE [auth b],
QG [auth j],
RA [auth A],
RC [auth G],
RD [auth C],
RE [auth b],
RF [auth W],
RG [auth j],
SA [auth A],
SB [auth M],
SC [auth G],
SD [auth f],
SE [auth b],
SF [auth V],
TA [auth A],
TB [auth M],
TC [auth G],
TD [auth f],
TE [auth a],
TF [auth V],
TG [auth i],
UB [auth M],
UC [auth G],
UD [auth f],
UE [auth a],
UF [auth V],
VA [auth R],
VB [auth L],
VC [auth G],
VD [auth f],
VE [auth a],
VF [auth V],
WA [auth R],
WB [auth L],
WD [auth f],
WE [auth a],
WF [auth V],
WG [auth h],
XA [auth R],
XB [auth L],
XC [auth G],
XD [auth f],
XF [auth V],
XG [auth h],
YA [auth R],
YB [auth L],
YD [auth e],
YF [auth V],
YG [auth h],
ZA [auth R],
ZB [auth K],
ZE [auth Z],
ZF [auth V],
ZG [auth h]
8-ANILINO-1-NAPHTHALENE SULFONATE
C16 H13 N O3 S
FWEOQOXTVHGIFQ-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
IB [auth P]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
FLC
Query on FLC

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SG [auth j]
UG [auth i]
VG [auth i]
WC [auth G]
XE [auth a]
SG [auth j],
UG [auth i],
VG [auth i],
WC [auth G],
XE [auth a],
YE [auth a],
ZD [auth e]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DB [auth Q]
FH [auth g]
JF [auth Y]
KD [auth E]
KE [auth c]
DB [auth Q],
FH [auth g],
JF [auth Y],
KD [auth E],
KE [auth c],
LE [auth c],
MC [auth I],
ME [auth c],
UA [auth A],
ZC [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
QF [auth X],
RB [auth N],
YC [auth G]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.85α = 90
b = 145.85β = 90
c = 385.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description