1ICJ | pdb_00001icj

PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)

PDB DOI: https://doi.org/10.2210/pdb1ICJ/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1998-03-12 Released: 1999-03-23
Deposition Author(s): Becker, A., Schlichting, I., Kabsch, W., Schultz, S., Wagner, A.F.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.230 (Depositor), 0.223 (DCC)
R-Value Work:
0.198 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of peptide deformylase and identification of the substrate binding site.

Becker, A., Schlichting, I., Kabsch, W., Schultz, S., Wagner, A.F.

(1998) J Biological Chem 273: 11413-11416

PubMed: 9565550 Search on PubMed
DOI: https://doi.org/10.1074/jbc.273.19.11413
Primary Citation Related Structures:
1BS7, 1ICJ

PubMed Abstract:
Peptide deformylase is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria. The Escherichia coli enzyme uses Fe2+ and nearly retains its activity on substitution of the metal ion by Ni2+. We have solved the structure of the Ni2+ enzyme at 1.9-A resolution by x-ray crystallography. Each of the three monomers in the asymmetric unit contains one Ni2+ ion and, in close proximity, one molecule of polyethylene glycol. Polyethylene glycol is shown to be a competitive inhibitor with a KI value of 6 mM with respect to formylmethionine under conditions similar to those used for crystallization. We have also solved the structure of the inhibitor-free enzyme at 2.5-A resolution. The two structures are identical within the estimated errors of the models. The hydrogen bond network stabilizing the active site involves nearly all conserved amino acid residues and well defined water molecules, one of which ligates to the tetrahedrally coordinated Ni2+ ion.

Organizational Affiliation

Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Jahnstrasse 29, 69120 Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 59.29 kDa
Atom Count: 4,424
Modeled Residue Count: 504
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE DEFORMYLASE	A, B, C	168	Escherichia coli K-12	Mutation(s): 0 Gene Names: DEF EC: 3.5.1.31 (PDB Primary Data), 3.5.1.88 (UniProt)
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12)) Explore P0A6K3 Go to UniProtKB: P0A6K3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6K3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], K [auth C]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth C] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth C] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], J [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230 (Depositor), 0.223 (DCC)
R-Value Work: 0.198 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.7	α = 90
b = 63.4	β = 120.6
c = 86.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-03-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-03-23
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Other