1MKZ | pdb_00001mkz

Crystal structure of MoaB protein at 1.6 A resolution.

PDB DOI: https://doi.org/10.2210/pdb1MKZ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2002-08-29 Released: 2003-04-22
Deposition Author(s): Sanishvili, R., Skarina, T., Joachimiak, A., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.219 (Depositor)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis.

Sanishvili, R., Beasley, S., Skarina, T., Glesne, D., Joachimiak, A., Edwards, A., Savchenko, A.

(2004) J Biological Chem 279: 42139-42146

PubMed: 15269205 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M407694200
Primary Citation Related Structures:
1MKZ

PubMed Abstract:
The crystal structure of Escherichia coli MoaB was determined by multiwavelength anomalous diffraction phasing and refined at 1.6-A resolution. The molecule displayed a modified Rossman fold. MoaB is assembled into a hexamer composed of two trimers. The monomers have high structural similarity with two proteins, MogA and MoeA, from the molybdenum cofactor synthesis pathway in E. coli, as well as with domains of mammalian gephyrin and plant Cnx1, which are also involved in molybdopterin synthesis. Structural comparison between these proteins and the amino acid conservation patterns revealed a putative active site in MoaB. The structural analysis of this site allowed to advance several hypothesis that can be tested in further studies.

Organizational Affiliation

Biosciences, Structural Biology Center, Midwest Center for Sructural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Macromolecule Content

Total Structure Weight: 38.73 kDa
Atom Count: 2,961
Modeled Residue Count: 341
Deposited Residue Count: 344
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum cofactor biosynthesis protein B	A, B	172	Escherichia coli	Mutation(s): 3 Gene Names: MoaB
UniProt
Find proteins for P0AEZ9 (Escherichia coli (strain K12)) Explore P0AEZ9 Go to UniProtKB: P0AEZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], L [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.219 (Depositor)
R-Value Work: 0.183 (Depositor)
R-Value Observed: 0.185 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.169	α = 90
b = 69.169	β = 90
c = 126.184	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CNS	refinement
WARP	model building
d*TREK	data scaling
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-04-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2003-04-22
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2024-03-06
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-11-06
Changes: Structure summary