2PC6 | pdb_00002pc6

Crystal structure of putative acetolactate synthase- small subunit from Nitrosomonas europaea

PDB DOI: https://doi.org/10.2210/pdb2PC6/pdb
Entry: 2PC6 supersedes: 2FGD

Classification: LYASE
Organism(s): Nitrosomonas europaea ATCC 19718
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-29 Released: 2007-04-10
Deposition Author(s): Petkowski, J.J., Chruszcz, M., Zimmerman, M.D., Zheng, H., Cymborowski, M.T., Skarina, T., Onopriyenko, O., Savchenko, A., Edwards, A., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.276 (Depositor), 0.273 (DCC)
R-Value Work:
0.205 (Depositor), 0.204 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.

Petkowski, J.J., Chruszcz, M., Zimmerman, M.D., Zheng, H., Skarina, T., Onopriyenko, O., Cymborowski, M.T., Koclega, K.D., Savchenko, A., Edwards, A., Minor, W.

(2007) Protein Sci 16: 1360-1367

PubMed: 17586771 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1110/ps.072793807
Primary Citation Related Structures:
2FGC, 2PC6

PubMed Abstract:
Crystal structures of two orthologs of the regulatory subunit of acetohydroxyacid synthase III (AHAS, EC 2.2.1.6) from Thermotoga maritima (TM0549) and Nitrosomonas europea (NE1324) were determined by single-wavelength anomalous diffraction methods with the use of selenomethionine derivatives at 2.3 A and 2.5 A, respectively. TM0549 and NE1324 share the same fold, and in both proteins the polypeptide chain contains two separate domains of a similar size. Each protein contains a C-terminal domain with ferredoxin-type fold and an N-terminal ACT domain, of which the latter is characteristic for several proteins involved in amino acid metabolism. The ferredoxin domain is stabilized by a calcium ion in the crystal structure of NE1324 and by a Mg(H2O)(6)2+ ion in TM0549. Both TM0549 and NE1324 form dimeric assemblies in the crystal lattice.

Organizational Affiliation

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908, USA.

Macromolecule Content

Total Structure Weight: 74.39 kDa
Atom Count: 5,145
Modeled Residue Count: 653
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable acetolactate synthase isozyme III (Small subunit)	A, B, C, D	165	Nitrosomonas europaea ATCC 19718	Mutation(s): 0 Gene Names: ilvH, NE1324 EC: 4.1.3.18 (PDB Primary Data), 2.2.1.6 (UniProt)
UniProt
Find proteins for Q82UZ2 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82UZ2 Go to UniProtKB: Q82UZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82UZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]
UNL Query on UNL Download:Ideal Coordinates CCD File	F [auth A], H [auth B], J [auth D]	Unknown ligand BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.276 (Depositor), 0.273 (DCC)
R-Value Work: 0.205 (Depositor), 0.204 (DCC)
R-Value Observed: 0.208 (Depositor)

Diffraction Data:

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.123	α = 90
b = 122.123	β = 90
c = 111.559	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
SOLVE	phasing
O	model building
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-3000	phasing
DM	phasing
RESOLVE	phasing
CCP4	phasing
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-04-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 2FGD

Revision History (Full details and data files)

Version 1.0: 2007-04-10
Type: Initial release
Version 1.1: 2007-10-09
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2012-02-01
Changes: Non-polymer description
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2024-11-13
Changes: Data collection, Refinement description, Structure summary