2HSJ | pdb_00002hsj

The structure of a putative platelet activating factor from Streptococcus pneumonia.

PDB DOI: https://doi.org/10.2210/pdb2HSJ/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-07-21 Released: 2006-09-19
Deposition Author(s): Cuff, M.E., Mulligan, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.193 (Depositor), 0.192 (DCC)
R-Value Work:
0.160 (Depositor), 0.159 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The structure of a putative platelet activating factor from Streptococcus pneumonia.

Cuff, M.E., Mulligan, R., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 99.02 kDa
Atom Count: 8,404
Modeled Residue Count: 849
Deposited Residue Count: 856
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative platelet activating factor	A, B, C, D	214	Streptococcus pneumoniae TIGR4	Mutation(s): 2 Gene Names: SP1450
UniProt
Find proteins for A0A0H2UQU7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQU7 Go to UniProtKB: A0A0H2UQU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UQU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] K [auth B] L [auth B] M [auth B] F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], O [auth C], R [auth D], S [auth D], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A] H [auth B] I [auth B] J [auth B] N [auth C] E [auth A], H [auth B], I [auth B], J [auth B], N [auth C], P [auth D], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.193 (Depositor), 0.192 (DCC)
R-Value Work: 0.160 (Depositor), 0.159 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.032	α = 90
b = 120.063	β = 99.48
c = 84.743	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
autoSHARP	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-09-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-09-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary