3OP1 | pdb_00003op1

Crystal Structure of Macrolide-efflux Protein SP_1110 from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb3OP1/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-08-31 Released: 2010-09-29
Deposition Author(s): Kim, Y., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.265 (Depositor), 0.282 (DCC)
R-Value Work:
0.198 (Depositor), 0.220 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Macrolide-efflux Protein SP_1110 from Streptococcus pneumoniae

Kim, Y., Li, H., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 107.64 kDa
Atom Count: 7,247
Modeled Residue Count: 861
Deposited Residue Count: 924
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide-efflux protein	A, B, C	308	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: SP_1110 EC: 2.7.7.2 (UniProt), 2.7.1.26 (UniProt)
UniProt
Find proteins for A0A0H2UPY5 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UPY5 Go to UniProtKB: A0A0H2UPY5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UPY5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain S [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth B]	F [auth A], K [auth A], P [auth B], S [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain S [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain T [auth C] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C]	D [auth A], M [auth B], N [auth B], T [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain V [auth C] SDF format, chain Q [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain E [auth A]	E [auth A] G [auth A] I [auth A] J [auth A] L [auth B] E [auth A], G [auth A], I [auth A], J [auth A], L [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.265 (Depositor), 0.282 (DCC)
R-Value Work: 0.198 (Depositor), 0.220 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.153	α = 90
b = 73.247	β = 112.48
c = 87.518	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary