5CYB | pdb_00005cyb

Structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb5CYB/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-30 Released: 2016-09-14
Deposition Author(s): Carrasco-Lopez, C., Abdullah, M.R., Hammerschmidt, S., Hermoso, J.A.
Funding Organization(s): the Government of Community of Madrid, German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.217 (Depositor), 0.236 (DCC)
R-Value Work:
0.194 (Depositor), 0.209 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Unraveling the function and structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae

Abdullah, M.R., Carrasco-Lopez, C., Saleh, M., Gomez, A., Petruschka, L., VoB, F., Pribyl, T., Hermoso, J.A., Hammerschmidt, S.

To be published.

Macromolecule Content

Total Structure Weight: 16.78 kDa
Atom Count: 779
Modeled Residue Count: 89
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein	A	152	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: ERS019416_00104, ERS019595_00220, ERS021447_05272, ERS022232_05596, ERS409134_00058, ERS409372_00175, ERS515225_00124

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.217 (Depositor), 0.236 (DCC)
R-Value Work: 0.194 (Depositor), 0.209 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.485	α = 90
b = 107.485	β = 90
c = 63.87	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Funding Organization	Location	Grant Number
the Government of Community of Madrid	Spain	BFU2011-25326
German Research Foundation	Germany	1870, HA3125/4-2

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description