3S4C | pdb_00003s4c

Lactose phosphorylase in complex with sulfate

PDB DOI: https://doi.org/10.2210/pdb3S4C/pdb

Classification: TRANSFERASE
Organism(s): Cellulomonas uda
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-05-19 Released: 2012-06-27
Deposition Author(s): Van Hoorebeke, A., Stout, J., Soetaert, W., Van Beeumen, J., Desmet, T., Savvides, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.214 (Depositor), 0.211 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3S4C

This is version 1.1 of the entry. See complete history.

Literature

Cellobiose phosphorylase: reconstructing the structural itinerary along the catalytic pathway

Van Hoorebeke, A., Stout, J., Soetaert, W., Van Beeumen, J., Desmet, T., Savvides, S.

To be published.

Macromolecule Content

Total Structure Weight: 91.68 kDa
Atom Count: 6,912
Modeled Residue Count: 822
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose Phosphorylase	A	822	Cellulomonas uda	Mutation(s): 2 EC: 2.4.1.20
UniProt
Find proteins for Q7WTR6 (Cellulomonas uda) Explore Q7WTR6 Go to UniProtKB: Q7WTR6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7WTR6
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.214 (Depositor), 0.211 (DCC)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.45	α = 90
b = 93.21	β = 90
c = 106.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Van Hoorebeke, A.

Van Beeumen, J.

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.