3G3P

The structure of the M53A Mutant of the Caulobacter crescentus CLPS in complex with a peptide containing an amino-terminal norleucine residue

PDB DOI: https://doi.org/10.2210/pdb3G3P/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Caulobacter vibrioides
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-02-02 Released: 2010-03-09
Deposition Author(s): Baker, T.A., Roman-Hernandez, G., Sauer, R.T., Grant, R.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.191
R-Value Work: 0.169
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Caulobacter crescentus ClpS in complex with various peptides

Roman-Hernandez, G., Grant, R.A., Sauer, R.T., Baker, T.A.

To be published.

Macromolecule Content

Total Structure Weight: 21.03 kDa
Atom Count: 1,725
Modelled Residue Count: 166
Deposited Residue Count: 180
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease adapter protein clpS	A, B	85	Caulobacter vibrioides	Mutation(s): 1 Gene Names: CC_2467, clpS
UniProt
Find proteins for Q9A5I0 (Caulobacter vibrioides (strain ATCC 19089 / CB15)) Explore Q9A5I0 Go to UniProtKB: Q9A5I0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9A5I0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide (NLE)LFVQRDSKE	C [auth D]	10	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE Query on NLE	C [auth D]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.191
R-Value Work: 0.169
R-Value Observed: 0.170
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.665	α = 90
b = 54.049	β = 110.44
c = 44.615	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Roman-Hernandez, G.

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations

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.