4I61 | pdb_00004i61

Crystal structure of a trimeric bacterial microcompartment shell protein PduB

PDB DOI: https://doi.org/10.2210/pdb4I61/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Limosilactobacillus reuteri SD2112
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-11-29 Released: 2014-03-26
Deposition Author(s): Pang, A.H., Pickersgill, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.200 (Depositor), 0.202 (DCC)
R-Value Work:
0.153 (Depositor), 0.157 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4I61

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

Literature

Propionaldehyde does not bind to PduB

Pang, A.H., Prentice, M.B., Pickersgill, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 81.15 kDa
Atom Count: 5,879
Modeled Residue Count: 682
Deposited Residue Count: 774
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propanediol utilization protein PduB	A, B, C	258	Limosilactobacillus reuteri SD2112	Mutation(s): 0 Gene Names: HMPREF0538_20934, pduB
UniProt
Find proteins for F8DQ39 (Limosilactobacillus reuteri (strain ATCC 55730 / SD2112)) Explore F8DQ39 Go to UniProtKB: F8DQ39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F8DQ39
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.200 (Depositor), 0.202 (DCC)
R-Value Work: 0.153 (Depositor), 0.157 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.01	α = 90
b = 119.55	β = 90
c = 147.09	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Pickersgill, R.W.

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Refinement description

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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.