2AFI

Crystal Structure of MgADP bound Av2-Av1 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history


Literature

Nitrogenase Complexes: Multiple Docking Sites for a Nucleotide Switch Protein

Tezcan, F.A.Kaiser, J.T.Mustafi, D.Walton, M.Y.Howard, J.B.Rees, D.C.

(2005) Science 309: 1377-1380

  • DOI: 10.1126/science.1115653
  • Primary Citation of Related Structures:  
    2AFH, 2AFI, 4WZB

  • PubMed Abstract: 
  • Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia ...

    Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron transfer rate, is coupled to the nucleotide state. More generally, stabilization of distinct docking geometries by different nucleotide states, as seen for nitrogenase, could enable nucleotide hydrolysis to drive the relative motion of protein partners in molecular motors and other systems.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 114-96, Pasadena, CA 91125, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron proteinA, C, I, K491Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifD
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
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Go to UniProtKB:  P07328
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron proteinB, D, J, L522Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifK
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
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Go to UniProtKB:  P07329
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrogenase iron protein 1E, F, G, H, M, N, O, P289Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifH1
EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii)
Explore P00459 
Go to UniProtKB:  P00459
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFN (Subject of Investigation/LOI)
Query on CFN

Download Ideal Coordinates CCD File 
JA [auth I], NA [auth K], R [auth A], W [auth C]FE(7)-MO-S(9)-N CLUSTER
Fe7 Mo N S9
OSSJGSCTDHHOOW-UHFFFAOYSA-N
 Ligand Interaction
CLF (Subject of Investigation/LOI)
Query on CLF

Download Ideal Coordinates CCD File 
LA [auth J], PA [auth L], U [auth B], X [auth D]FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth F], FA [auth G], HA [auth H], RA [auth M], UA [auth N], WA [auth O], Z [auth E], ZA [auth P]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
BA [auth F], EA [auth G], TA [auth N], YA [auth P]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
HCA (Subject of Investigation/LOI)
Query on HCA

Download Ideal Coordinates CCD File 
IA [auth I], MA [auth K], Q [auth A], V [auth C]3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
KA [auth J], OA [auth L], S [auth B], T [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth F], DA [auth G], GA [auth H], QA [auth M], SA [auth N], VA [auth O], XA [auth P], Y [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.915α = 73.69
b = 141.432β = 79.37
c = 165.549γ = 76.58
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations