4WXL | pdb_00004wxl

Crystal structure of a peptide deformylase from Haemophilus influenzae complex with Actinonin

PDB DOI: https://doi.org/10.2210/pdb4WXL/pdb

Classification: HYDROLASE
Organism(s): Haemophilus influenzae 86-028NP
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-14 Released: 2015-11-18
Deposition Author(s): Kishor, C., Addlagatta, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.241 (Depositor), 0.254 (DCC)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.175 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a peptide deformylase from Haemophilus influenzae complex with Actinonin

Kishor, C., Addlagatta, A.

To be published.

Macromolecule Content

Total Structure Weight: 78.11 kDa
Atom Count: 5,420
Modeled Residue Count: 655
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C, D	169	Haemophilus influenzae 86-028NP	Mutation(s): 0 Gene Names: def, NTHI0725 EC: 3.5.1.88
UniProt
Find proteins for Q4QMV6 (Haemophilus influenzae (strain 86-028NP)) Explore Q4QMV6 Go to UniProtKB: Q4QMV6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QMV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BB2 Query on BB2 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.241 (Depositor), 0.254 (DCC)
R-Value Work: 0.172 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.201	α = 90
b = 79.85	β = 97.99
c = 98.168	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
DENZO	data scaling
MOLREP	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-18
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.