4H5G

Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 2

PDB DOI: https://doi.org/10.2210/pdb4H5G/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae str. Canada MDR_19A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-18 Released: 2012-10-03
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Kudritska, M., Minasov, G., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.186
R-Value Work: 0.156
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 2

Stogios, P.J., Wawrzak, Z., Kudritska, M., Minasov, G., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 53.76 kDa
Atom Count: 4,262
Modelled Residue Count: 480
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC superfamily ATP binding cassette transporter, binding protein	A, B	243	Streptococcus pneumoniae str. Canada MDR_19A	Mutation(s): 0 Gene Names: HMPREF0837_11153, SpneCM_010100001092
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARG Query on ARG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B]	L [auth A], Q [auth B]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B]	D [auth A], E [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B]	C [auth A], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B]	H [auth A], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B]	I [auth A], J [auth A], K [auth A], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.186
R-Value Work: 0.156
R-Value Observed: 0.157
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M34H5G

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.6	α = 90
b = 183.94	β = 90
c = 62.024	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-03

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-10-03
Type: Initial release
Version 1.1: 2014-12-17
Changes: Other
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description