3LYC

Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution

PDB DOI: https://doi.org/10.2210/pdb3LYC/pdb

Classification: CELL ADHESION
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-26 Released: 2010-03-16
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.280
R-Value Work: 0.244
R-Value Observed: 0.246

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 419.64 kDa
Atom Count: 29,713
Modelled Residue Count: 3,827
Deposited Residue Count: 3,856
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative pectinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	241	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_3084
UniProt
Find proteins for A6LGH6 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LGH6 Go to UniProtKB: A6LGH6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LGH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.280
R-Value Work: 0.244
R-Value Observed: 0.246
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33LYC

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.116	α = 90
b = 104.606	β = 90
c = 393.587	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.