6ICA | pdb_00006ica

The crystal structure of Legionella pneumophila LapA aminopeptidase

PDB DOI: https://doi.org/10.2210/pdb6ICA/pdb

Classification: HYDROLASE
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-05 Released: 2019-11-06
Deposition Author(s): Honghua, G., Nannan, Z.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.143 (Depositor), 0.140 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of Legionella pneumophila LapA aminopeptidase

Honghua, G., Nannan, Z.

To be published.

Macromolecule Content

Total Structure Weight: 146.52 kDa
Atom Count: 9,489
Modeled Residue Count: 1,115
Deposited Residue Count: 1,290
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A, B, C	430	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: lpg2814
UniProt
Find proteins for Q5ZRR6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRR6 Go to UniProtKB: Q5ZRR6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZRR6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth C]	D [auth A] K [auth A] L [auth A] M [auth B] N [auth B] D [auth A], K [auth A], L [auth A], M [auth B], N [auth B], R [auth B], S [auth B], T [auth C], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Y [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Y [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	E [auth A], F [auth A], O [auth B], U [auth C], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	G [auth A] H [auth A] P [auth B] Q [auth B] W [auth C] G [auth A], H [auth A], P [auth B], Q [auth B], W [auth C], X [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.143 (Depositor), 0.140 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.424	α = 90
b = 121.913	β = 90
c = 130.812	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-06

Deposition Author(s):

Honghua, G.

Nannan, Z.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31400641
National Natural Science Foundation of China	China	31270770

Revision History (Full details and data files)

Version 1.0: 2019-11-06
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary