1I6N | pdb_00001i6n

1.8 A Crystal structure of IOLI protein with a binding zinc atom

PDB DOI: https://doi.org/10.2210/pdb1I6N/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2001-03-02 Released: 2002-03-13
Deposition Author(s): Zhang, R.G., Dementiva, I., Collart, F., Quaite-Randall, E., Joachimiak, A., Alkire, R., Maltsev, N., Korolev, O., Dieckman, L., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding.

Zhang, R.G., Dementieva, I., Duke, N., Collart, F., Quaite-Randall, E., Alkire, R., Dieckman, L., Maltsev, N., Korolev, O., Joachimiak, A.

(2002) Proteins 48: 423-426

PubMed: 12112707 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.10159
Primary Citation Related Structures:
1I60, 1I6N

Organizational Affiliation

Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Macromolecule Content

Total Structure Weight: 32.04 kDa
Atom Count: 2,404
Modeled Residue Count: 278
Deposited Residue Count: 278
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IOLI PROTEIN	A	278	Bacillus subtilis	Mutation(s): 6 Gene Names: IOLI OR B65B EC: 5.3.99.11
UniProt
Find proteins for P42419 (Bacillus subtilis (strain 168)) Explore P42419 Go to UniProtKB: P42419
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42419
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.80 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.201 (Depositor), 0.201 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.015	α = 90
b = 104.616	β = 90
c = 48.462	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
HKL-2000	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-03-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2002-03-13
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-11-06
Changes: Structure summary