1NY1 | pdb_00001ny1

CRYSTAL STRUCTURE OF B. SUBTILIS POLYSACCHARIDE DEACETYLASE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR127.

PDB DOI: https://doi.org/10.2210/pdb1NY1/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-02-11 Released: 2003-03-18
Deposition Author(s): Forouhar, F., Edstrom, W., Khan, J., Ma, L., Chiang, Y., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.212 (Depositor), 0.203 (DCC)
R-Value Work:
0.182 (Depositor), 0.200 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Polysaccharide Deacetylase (PDAA_BACSU) from B. Subtilis (Pdaa_Bacsu) Northeast Structural Genomics Research Consortium (Nesg) Target Sr127

Forouhar, F., Edstrom, W., Khan, J., Ma, L., Chiang, Y., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 56.04 kDa
Atom Count: 4,382
Modeled Residue Count: 470
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable polysaccharide deacetylase pdaA	A, B	240	Bacillus subtilis	Mutation(s): 4 Gene Names: PdaA EC: 3.5.1
UniProt
Find proteins for O34928 (Bacillus subtilis (strain 168)) Explore O34928 Go to UniProtKB: O34928
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34928
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A, B	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.212 (Depositor), 0.203 (DCC)
R-Value Work: 0.182 (Depositor), 0.200 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.112	α = 90
b = 88.112	β = 90
c = 120.645	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-03-18

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2003-03-18
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary