3G3P | pdb_00003g3p

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 (Depositor), 0.177 (DCC)
R-Value Work:
0.169 (Depositor), 0.153 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3G3P

This is version 1.4 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
Modeled Residue Count: 166
Deposited Residue Count: 180
Unique protein chains: 2

Macromolecules

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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 / CIP 103742 / CB 15)) Explore Q9A5I0 Go to UniProtKB: Q9A5I0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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] mmCIF 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 (Depositor), 0.177 (DCC)
R-Value Work: 0.169 (Depositor), 0.153 (DCC)
R-Value Observed: 0.170 (Depositor)

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

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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
Version 1.4: 2024-10-30
Changes: Data collection, Structure summary

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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.