8R39 | pdb_00008r39

Full-length LpMIP mutant Y16F

PDB DOI: https://doi.org/10.2210/pdb8R39/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Legionella pneumophila
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-11-08 Released: 2024-11-20
Deposition Author(s): Whittaker, J.J., Guskov, A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.271 (Depositor), 0.294 (DCC)
R-Value Work:
0.218 (Depositor), 0.251 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8R39

This is version 1.0 of the entry. See complete history.

Literature

Full-length LpMIP mutant Y16F

Whittaker, J.J., Guskov, A.

To be published.

Macromolecule Content

Total Structure Weight: 23.1 kDa
Atom Count: 1,681
Modeled Residue Count: 208
Deposited Residue Count: 208
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A [auth C]	208	Legionella pneumophila	Mutation(s): 1 Gene Names: C3927_03235 EC: 5.2.1.8
UniProt
Find proteins for A5IGB8 (Legionella pneumophila (strain Corby)) Explore A5IGB8 Go to UniProtKB: A5IGB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5IGB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C]	E [auth C], F [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain C SDF format, chain B [auth C] MOL2 format, chain G [auth C] MOL2 format, chain C MOL2 format, chain B [auth C] mmCIF format, chain G [auth C] mmCIF format, chain C mmCIF format, chain B [auth C]	B [auth C], C, G [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth C] Focus chain C Focus chain G [auth C] Interactions & Density Focus chain B [auth C] Focus chain C Focus chain G [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271 (Depositor), 0.294 (DCC)
R-Value Work: 0.218 (Depositor), 0.251 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.444	α = 90
b = 78.444	β = 90
c = 105.176	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Whittaker, J.J.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	390713860

Revision History (Full details and data files)

Version 1.0: 2024-11-20
Type: Initial release

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