7AP5 | pdb_00007ap5

Crystal structure of phycoerythrin from cyanobacterium Nostoc sp. WR13 contains multiple stacks of hexameric assemblies which resemble the rods of phycobilisome.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.225 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.188 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

The crystal stacks of hexameric assemblies of phycoerythrin from cyanobacterium Nostoc sp. WR13 resemble rods of phycobilisome

Patel, H.M., Roszak, A.W., Liu, H., Gross, M.L., Blankenship, R.E., Madamwar, D., Cogdell, R.J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 355.85 kDa 
  • Atom Count: 26,483 
  • Modeled Residue Count: 2,784 
  • Deposited Residue Count: 2,784 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha subunit of cyanobacterial protein phycoerythrin164Nostoc sp. WR13Mutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta subunit of cyanobacterial protein phycoerythrin184Nostoc sp. WR13Mutation(s): 0 

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEB
(Subject of Investigation/LOI)

Query on PEB


Download:Ideal Coordinates CCD File
AC [auth DDD]
AD [auth EEE]
AH [auth JJJ]
BC [auth DDD]
BD [auth EEE]
AC [auth DDD],
AD [auth EEE],
AH [auth JJJ],
BC [auth DDD],
BD [auth EEE],
EB [auth CCC],
EF [auth HHH],
FB [auth CCC],
FF [auth HHH],
FG [auth III],
GF [auth HHH],
GG [auth III],
GL [auth PPP],
HA [auth BBB],
HL [auth PPP],
IA [auth BBB],
IL [auth PPP],
JA [auth BBB],
JI [auth LLL],
JJ [auth MMM],
KI [auth LLL],
KJ [auth MMM],
LI [auth LLL],
ME [auth GGG],
NE [auth GGG],
Q [auth AAA],
QD [auth FFF],
R [auth AAA],
RD [auth FFF],
SD [auth FFF],
SH [auth KKK],
TH [auth KKK],
TK [auth OOO],
UK [auth OOO],
XJ [auth NNN],
YG [auth JJJ],
YJ [auth NNN],
ZB [auth DDD],
ZG [auth JJJ],
ZJ [auth NNN]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
RWB

Query on RWB


Download:Ideal Coordinates CCD File
KA [auth BBB],
MI [auth LLL]		dodecaethylene glycol monomethyl ether
C25 H52 O13
PLQZJIIDLZRWBG-UHFFFAOYSA-N
PE5

Query on PE5


Download:Ideal Coordinates CCD File
AK [auth NNN]3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
PE8

Query on PE8


Download:Ideal Coordinates CCD File
LA [auth BBB]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
P33

Query on P33


Download:Ideal Coordinates CCD File
BH [auth JJJ]
CC [auth DDD]
DC [auth DDD]
HF [auth HHH]
IF [auth HHH]
BH [auth JJJ],
CC [auth DDD],
DC [auth DDD],
HF [auth HHH],
IF [auth HHH],
TD [auth FFF]
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G

Query on P6G


Download:Ideal Coordinates CCD File
EC [auth DDD]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE

Query on 1PE


Download:Ideal Coordinates CCD File
CD [auth EEE]
CH [auth JJJ]
DF [auth HHH]
DH [auth JJJ]
FC [auth DDD]
CD [auth EEE],
CH [auth JJJ],
DF [auth HHH],
DH [auth JJJ],
FC [auth DDD],
JL [auth PPP],
MA [auth BBB],
NA [auth BBB],
ND [auth FFF],
NI [auth LLL],
OA [auth BBB],
XG [auth JJJ]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4

Query on PG4


Download:Ideal Coordinates CCD File
BK [auth NNN]
CK [auth NNN]
DK [auth NNN]
EH [auth JJJ]
GB [auth CCC]
BK [auth NNN],
CK [auth NNN],
DK [auth NNN],
EH [auth JJJ],
GB [auth CCC],
GC [auth DDD],
HC [auth DDD],
JF [auth HHH],
KF [auth HHH],
KL [auth PPP],
LJ [auth MMM],
LL [auth PPP],
MJ [auth MMM],
NJ [auth MMM],
OD [auth FFF],
OE [auth GGG],
OI [auth LLL],
PE [auth GGG],
PI [auth LLL],
QE [auth GGG],
QI [auth LLL],
S [auth AAA],
T [auth AAA],
U [auth AAA],
UD [auth FFF],
UH [auth KKK],
UJ [auth MMM],
VD [auth FFF],
VH [auth KKK],
VJ [auth NNN],
VK [auth OOO],
WD [auth FFF],
WH [auth KKK],
WJ [auth NNN]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE


Download:Ideal Coordinates CCD File
AA [auth AAA]
CB [auth BBB]
CF [auth GGG]
DD [auth EEE]
DG [auth HHH]
AA [auth AAA],
CB [auth BBB],
CF [auth GGG],
DD [auth EEE],
DG [auth HHH],
ED [auth EEE],
EK [auth NNN],
FD [auth EEE],
FH [auth JJJ],
FK [auth NNN],
GD [auth EEE],
GH [auth JJJ],
GK [auth NNN],
HB [auth CCC],
HG [auth III],
HJ [auth LLL],
HK [auth NNN],
IB [auth CCC],
IC [auth DDD],
IG [auth III],
IJ [auth LLL],
JB [auth CCC],
JC [auth DDD],
JG [auth III],
KB [auth CCC],
KC [auth DDD],
KG [auth III],
LB [auth CCC],
LF [auth HHH],
MF [auth HHH],
ML [auth PPP],
NF [auth HHH],
OF [auth HHH],
OJ [auth MMM],
PA [auth BBB],
PF [auth HHH],
PJ [auth MMM],
QA [auth BBB],
RE [auth GGG],
RI [auth LLL],
SE [auth GGG],
SI [auth LLL],
TE [auth GGG],
V [auth AAA],
W [auth AAA],
WG [auth JJJ],
WK [auth OOO],
X [auth AAA],
XD [auth FFF],
XH [auth KKK],
XK [auth OOO],
Y [auth AAA],
YD [auth FFF],
YH [auth KKK],
YK [auth OOO],
Z [auth AAA],
ZD [auth FFF]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
AE [auth FFF]
AI [auth KKK]
AJ [auth LLL]
AL [auth OOO]
BA [auth AAA]
AE [auth FFF],
AI [auth KKK],
AJ [auth LLL],
AL [auth OOO],
BA [auth AAA],
BE [auth FFF],
BI [auth KKK],
BL [auth OOO],
CA [auth AAA],
CE [auth FFF],
CI [auth KKK],
CL [auth OOO],
DB [auth BBB],
DE [auth FFF],
DI [auth KKK],
EE [auth FFF],
EG [auth III],
FL [auth PPP],
HH [auth JJJ],
IH [auth JJJ],
IK [auth NNN],
JH [auth JJJ],
JK [auth NNN],
KK [auth NNN],
LC [auth DDD],
LD [auth EEE],
LG [auth III],
MB [auth CCC],
MC [auth DDD],
MD [auth EEE],
MG [auth III],
NB [auth CCC],
NC [auth DDD],
NG [auth III],
NL [auth PPP],
OB [auth CCC],
OC [auth DDD],
OG [auth III],
OL [auth PPP],
PB [auth CCC],
PG [auth III],
PL [auth PPP],
QB [auth CCC],
QF [auth HHH],
QJ [auth MMM],
QL [auth PPP],
RA [auth BBB],
RB [auth CCC],
RF [auth HHH],
RJ [auth MMM],
RL [auth PPP],
SA [auth BBB],
SB [auth CCC],
SF [auth HHH],
SJ [auth MMM],
SL [auth PPP],
TA [auth BBB],
TF [auth HHH],
TI [auth LLL],
UA [auth BBB],
UE [auth GGG],
UF [auth HHH],
UI [auth LLL],
VA [auth BBB],
VE [auth GGG],
VI [auth LLL],
WA [auth BBB],
WB [auth CCC],
WE [auth GGG],
WI [auth LLL],
XE [auth GGG],
XI [auth LLL],
YB [auth CCC],
YE [auth GGG],
YI [auth LLL],
ZC [auth DDD],
ZH [auth KKK],
ZI [auth LLL],
ZK [auth OOO]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
AB [auth BBB]
AF [auth GGG]
AG [auth HHH]
CJ [auth LLL]
DA [auth AAA]
AB [auth BBB],
AF [auth GGG],
AG [auth HHH],
CJ [auth LLL],
DA [auth AAA],
DJ [auth LLL],
DL [auth OOO],
EA [auth AAA],
EI [auth KKK],
FI [auth KKK],
GE [auth FFF],
GI [auth KKK],
HE [auth FFF],
IE [auth FFF],
JE [auth FFF],
KE [auth FFF],
KH [auth JJJ],
LH [auth JJJ],
MH [auth JJJ],
NH [auth JJJ],
OH [auth JJJ],
OK [auth NNN],
PK [auth NNN],
QH [auth JJJ],
QK [auth NNN],
RC [auth DDD],
RG [auth III],
RK [auth NNN],
SC [auth DDD],
SG [auth III],
SK [auth NNN],
TB [auth CCC],
TC [auth DDD],
TG [auth III],
UB [auth CCC],
UC [auth DDD],
UL [auth PPP],
VC [auth DDD],
VL [auth PPP],
WC [auth DDD],
WL [auth PPP],
XA [auth BBB],
XB [auth CCC],
XF [auth HHH],
YA [auth BBB],
YF [auth HHH],
ZA [auth BBB],
ZE [auth GGG],
ZF [auth HHH]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO


Download:Ideal Coordinates CCD File
BJ [auth LLL]
FE [auth FFF]
HD [auth EEE]
ID [auth EEE]
LK [auth NNN]
BJ [auth LLL],
FE [auth FFF],
HD [auth EEE],
ID [auth EEE],
LK [auth NNN],
MK [auth NNN],
NK [auth NNN],
PC [auth DDD],
PD [auth FFF],
QC [auth DDD],
QG [auth III],
TL [auth PPP],
UG [auth III],
VF [auth HHH],
WF [auth HHH]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3

Query on NO3


Download:Ideal Coordinates CCD File
BB [auth BBB]
BF [auth GGG]
BG [auth HHH]
CG [auth HHH]
EJ [auth LLL]
BB [auth BBB],
BF [auth GGG],
BG [auth HHH],
CG [auth HHH],
EJ [auth LLL],
EL [auth OOO],
FA [auth AAA],
FJ [auth LLL],
GA [auth AAA],
GJ [auth LLL],
HI [auth KKK],
II [auth KKK],
JD [auth EEE],
KD [auth EEE],
LE [auth FFF],
PH [auth JJJ],
RH [auth JJJ],
TJ [auth MMM],
VB [auth CCC],
VG [auth III],
XC [auth DDD],
XL [auth PPP],
YC [auth DDD]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B [auth BBB]
D [auth DDD]
F [auth FFF]
H [auth HHH]
J [auth JJJ]
B [auth BBB],
D [auth DDD],
F [auth FFF],
H [auth HHH],
J [auth JJJ],
L [auth LLL],
N [auth NNN],
P [auth PPP]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.225 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.188 (DCC) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.759α = 90
b = 192.759β = 90
c = 524.486γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
pointlessdata scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0001035 (Office of Basic Energy Sciences)
Department of Biotechnology (DBT, India)IndiaBT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship)
Department of Biotechnology (DBT, India)IndiaBT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship)

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description