2YNM

Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a

Structural Biology Knowledgebase: 2YNM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YNM

Classification: OXIDOREDUCTASE

Total Structure Weight: 175517.45

Macromolecule Entities
Molecule Chains Length Organism Details
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN A, B 301 Prochlorococcus marinus EC#: 1.18 IUBMB 1.3.7.7 IUBMB
Gene Name(s): chlL Pro_0544
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N C 426 Prochlorococcus marinus EC#: 1.18 IUBMB 1.3.7.7 IUBMB
Gene Name(s): chlN Pro_0546
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B D 530 Prochlorococcus marinus EC#: 1.18 IUBMB 1.3.7.7 IUBMB
Gene Name(s): chlB Pro_0545

Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1PE
Query on 1PE

A PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ADP
Query on ADP

A, B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
AF3
Query on AF3

A, B ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
Ligand Explorer
 
JSmol
EPE
Query on EPE

A, B, D 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A, C, D GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
K
Query on K

D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PMR
Query on PMR

C Protochlorophyllide
C35 H32 Mg N4 O5
ZHFORNQMLKGQNN-DEOLMCFKDB
Ligand Explorer
 
JSmol
SF4
Query on SF4

A, C IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.199
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 308.40 α = 90.00
b = 74.11 β = 91.24
c = 74.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-16
  • Released Date: 2013-01-30
  • Deposition author(s): Krausze, J., Lange, C., Heinz, D.W., Moser, J.

Revision History

  • 2013-03-06
    Type: Citation | Details: JRNL