1LA2 | pdb_00001la2

Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase

PDB DOI: https://doi.org/10.2210/pdb1LA2/pdb

Classification: ISOMERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-03-27 Released: 2002-04-10
Deposition Author(s): Kniewel, R., Buglino, J.A., Shen, V., Chadna, T., Beckwith, A., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.280 (Depositor), 0.228 (DCC)
R-Value Work:
0.224 (Depositor), 0.227 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase

Kniewel, R., Buglino, J.A., Shen, V., Chadna, T., Beckwith, A., Lima, C.D.

(2002) J Struct Funct Genomics 2: 129-134

PubMed: 12836703 Search on PubMed
DOI: https://doi.org/10.1023/a:1021293408654
Primary Citation Related Structures:
1LA2

PubMed Abstract:
The New York Structural Genomics Research Consortium has targeted highly conserved but uncharacterized enzyme families for structure determination. As part of this effort, the 2.65-A crystal structure has been determined for Saccharomyces cerevisiae myo-inositol 1-phosphate synthase (MIP), an essential enzyme that catalyzes critical steps in inositol biosynthesis. The structure determination of four independent monomers in the asymmetric unit (240 kDa) reveals atomic details and residue composition for the partially closed NAD-containing active sites in apo-configuration. The structure further reveals extensive interactions involved in tetrameric assembly of the enzyme complex.

Organizational Affiliation

Biochemistry Department and Structural Biology Program, Weill Medical College of Cornell University, New York, NY 10021, USA.

Macromolecule Content

Total Structure Weight: 243.36 kDa
Atom Count: 17,040
Modeled Residue Count: 2,056
Deposited Residue Count: 2,132
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myo-inositol-1-phosphate synthase	A, B, C, D	533	Saccharomyces cerevisiae	Mutation(s): 10 Gene Names: INO1 EC: 5.5.1.4
UniProt
Find proteins for P11986 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11986 Go to UniProtKB: P11986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11986
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [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: 2.65 Å
R-Value Free: 0.280 (Depositor), 0.228 (DCC)
R-Value Work: 0.224 (Depositor), 0.227 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.693	α = 90
b = 187.346	β = 90
c = 98.954	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-04-10

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2002-04-10
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: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Structure summary