4L1N | pdb_00004l1n

Crystal structure of a putative conserved lipoprotein (NT01CX_1156) from Clostridium novyi NT at 2.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb4L1N/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Clostridium novyi NT
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-03 Released: 2013-06-26
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.201 (Depositor), 0.225 (DCC)
R-Value Work:
0.198 (Depositor), 0.196 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4L1N

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

Literature

Crystal structure of a putative conserved lipoprotein (NT01CX_1156) from Clostridium novyi NT at 2.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 23.6 kDa
Atom Count: 1,288
Modeled Residue Count: 161
Deposited Residue Count: 206
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved lipoprotein, putative	A	206	Clostridium novyi NT	Mutation(s): 0 Gene Names: NT01CX_1156
UniProt
Find proteins for A0PXY7 (Clostridium novyi (strain NT)) Explore A0PXY7 Go to UniProtKB: A0PXY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0PXY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.201 (Depositor), 0.225 (DCC)
R-Value Work: 0.198 (Depositor), 0.196 (DCC)
R-Value Observed: 0.198 (Depositor)

Diffraction Data:

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.87	α = 90
b = 146.87	β = 90
c = 125.97	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-06-26
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-11-06
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.