2AFI | pdb_00002afi

Crystal Structure of MgADP bound Av2-Av1 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.270 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1126/science.1115653
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 721.73 kDa 
  • Atom Count: 48,501 
  • Modeled Residue Count: 6,137 
  • Deposited Residue Count: 6,364 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein
A, C, I, K
491Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07328
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein
B, D, J, L
522Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Entity Groups
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UniProt GroupP07329
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase iron protein 1
E, F, G, H, M
E, F, G, H, M, N, O, P
289Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P00459 (Azotobacter vinelandii)
Explore P00459 
Go to UniProtKB:  P00459
Entity Groups
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UniProt GroupP00459
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CFN

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
CLF

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-UHFFFAOYSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
CA [auth F]
FA [auth G]
HA [auth H]
RA [auth M]
UA [auth N]
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
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-UHFFFAOYSA-N
HCA

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
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
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth F]
DA [auth G]
GA [auth H]
QA [auth M]
SA [auth N]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.270 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
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
  • Version 1.4: 2023-08-23
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description