6HIF

Kuenenia stuttgartiensis hydrazine dehydrogenase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A 192-heme electron transfer network in the hydrazine dehydrogenase complex.

Akram, M.Dietl, A.Mersdorf, U.Prinz, S.Maalcke, W.Keltjens, J.Ferousi, C.de Almeida, N.M.Reimann, J.Kartal, B.Jetten, M.S.M.Parey, K.Barends, T.R.M.

(2019) Sci Adv 5: eaav4310-eaav4310

  • DOI: 10.1126/sciadv.aav4310
  • Primary Citation of Related Structures:  
    6HIF

  • PubMed Abstract: 
  • Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process ...

    Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrazine dehydrogenase582Candidatus Kuenenia stuttgartiensisMutation(s): 0 
Gene Names: kustc0694
EC: 1.7.2.8
UniProt
Find proteins for Q1PW30 (Kuenenia stuttgartiensis)
Explore Q1PW30 
Go to UniProtKB:  Q1PW30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1PW30
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
hdh assembly factor Kustc1130114Candidatus Kuenenia stuttgartiensisMutation(s): 0 
Gene Names: KSMBR1_2889
UniProt
Find proteins for A0A2C9CI58 (Kuenenia stuttgartiensis)
Explore A0A2C9CI58 
Go to UniProtKB:  A0A2C9CI58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2C9CI58
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
AB [auth A],
AC [auth C],
AD [auth E],
AG [auth L],
AH [auth N],
AB [auth A],
AC [auth C],
AD [auth E],
AG [auth L],
AH [auth N],
AI [auth Q],
AJ [auth S],
AK [auth V],
AL [auth X],
BB [auth A],
BC [auth C],
BG [auth L],
BH [auth N],
BI [auth Q],
BJ [auth S],
BK [auth V],
BL [auth X],
CB [auth A],
CC [auth C],
CG [auth L],
CI [auth Q],
CJ [auth S],
CK [auth V],
DB [auth A],
DC [auth C],
DD [auth F],
DE [auth I],
DI [auth Q],
DK [auth V],
EB [auth A],
EC [auth C],
ED [auth F],
EE [auth I],
EF [auth J],
EI [auth Q],
EK [auth V],
FB [auth A],
FC [auth C],
FD [auth F],
FE [auth I],
FF [auth K],
FH [auth O],
FI [auth Q],
FJ [auth S],
FK [auth V],
GB [auth A],
GD [auth F],
GE [auth I],
GF [auth K],
GH [auth O],
GI [auth Q],
GJ [auth T],
GK [auth V],
HD [auth F],
HE [auth I],
HF [auth K],
HH [auth O],
HJ [auth T],
ID [auth F],
IE [auth I],
IF [auth K],
IG [auth M],
IH [auth O],
IJ [auth T],
JC [auth D],
JD [auth F],
JE [auth I],
JF [auth K],
JG [auth M],
JH [auth O],
JJ [auth T],
KA [auth G],
KC [auth D],
KD [auth F],
KE [auth I],
KF [auth K],
KG [auth M],
KH [auth O],
KJ [auth T],
KK [auth V],
LA [auth G],
LC [auth D],
LF [auth K],
LG [auth M],
LH [auth O],
LI [auth R],
LJ [auth T],
LK [auth W],
MA [auth G],
MC [auth D],
MF [auth K],
MG [auth M],
MH [auth O],
MI [auth R],
MJ [auth T],
MK [auth W],
NA [auth G],
NB [auth A],
NC [auth D],
ND [auth H],
NG [auth M],
NI [auth R],
NJ [auth T],
NK [auth W],
OA [auth G],
OB [auth B],
OC [auth D],
OD [auth H],
OG [auth M],
OI [auth R],
OK [auth W],
PA [auth G],
PB [auth B],
PC [auth D],
PD [auth H],
PI [auth R],
PJ [auth U],
PK [auth W],
QA [auth G],
QB [auth B],
QD [auth H],
QH [auth P],
QI [auth R],
QJ [auth U],
QK [auth W],
RB [auth B],
RD [auth H],
RH [auth P],
RI [auth R],
RJ [auth U],
RK [auth W],
SB [auth B],
SC [auth D],
SD [auth H],
SE [auth J],
SH [auth P],
SI [auth R],
SJ [auth U],
SK [auth W],
TB [auth B],
TC [auth E],
TD [auth H],
TE [auth J],
TG [auth M],
TH [auth P],
TJ [auth U],
UB [auth B],
UC [auth E],
UD [auth H],
UE [auth J],
UG [auth N],
UH [auth P],
UJ [auth U],
UK [auth X],
VB [auth B],
VC [auth E],
VE [auth J],
VF [auth L],
VG [auth N],
VH [auth P],
VJ [auth U],
VK [auth X],
WC [auth E],
WE [auth J],
WF [auth L],
WG [auth N],
WH [auth P],
WI [auth S],
WJ [auth U],
WK [auth X],
XC [auth E],
XE [auth J],
XF [auth L],
XG [auth N],
XI [auth S],
XK [auth X],
YB [auth C],
YC [auth E],
YE [auth J],
YF [auth L],
YG [auth N],
YH [auth P],
YI [auth S],
YK [auth X],
ZA [auth G],
ZB [auth C],
ZC [auth E],
ZF [auth L],
ZG [auth N],
ZH [auth Q],
ZI [auth S],
ZK [auth X]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SO4
Query on SO4

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AF [auth J],
BD [auth E],
BF [auth J],
CD [auth E],
CH [auth N],
AF [auth J],
BD [auth E],
BF [auth J],
CD [auth E],
CH [auth N],
CL [auth X],
DG [auth L],
DH [auth N],
DJ [auth S],
DL [auth X],
EG [auth L],
EH [auth N],
EJ [auth S],
EL [auth X],
FG [auth L],
GC [auth C],
GG [auth L],
GL [auth Y],
HB [auth A],
HC [auth C],
HI [auth Q],
HK [auth V],
HL [auth Y],
IB [auth A],
IC [auth C],
II [auth Q],
IK [auth V],
IL [auth a],
JB [auth A],
JI [auth Q],
JK [auth V],
JL [auth c],
LD [auth F],
LE [auth I],
MD [auth F],
ME [auth I],
NE [auth I],
NF [auth K],
NH [auth O],
OE [auth I],
OF [auth K],
OH [auth O],
OJ [auth T],
PF [auth K],
PG [auth M],
PH [auth O],
QC [auth D],
QG [auth M],
RA [auth G],
RG [auth M],
SA [auth G],
SG [auth M],
TA [auth G],
TI [auth R],
TK [auth W],
UA [auth G],
UI [auth R],
VA [auth G],
VD [auth H],
VI [auth R],
WA [auth G],
WB [auth B],
WD [auth H],
XB [auth B],
XD [auth H],
XH [auth P],
XJ [auth U],
YD [auth H],
YJ [auth U],
ZD [auth H],
ZE [auth J],
ZJ [auth U]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AE [auth H],
BE [auth H],
CF [auth J],
DF [auth J],
HG [auth L],
AE [auth H],
BE [auth H],
CF [auth J],
DF [auth J],
HG [auth L],
KB [auth A],
LB [auth A],
MB [auth A],
PE [auth I],
QE [auth I],
QF [auth K],
RC [auth D],
RE [auth I],
RF [auth K],
SF [auth K],
TF [auth K],
XA [auth G],
YA [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
CE [auth H],
FL [auth X],
KI [auth Q],
UF [auth K]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.86α = 90
b = 211.86β = 90
c = 398.57γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references