4H5F

Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 1

PDB DOI: https://doi.org/10.2210/pdb4H5F/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: 1.90 Å
R-Value Free: 0.200
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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 1

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: 109.56 kDa
Atom Count: 8,142
Modelled Residue Count: 959
Deposited Residue Count: 972
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, C, D	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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARG Query on ARG Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain YA [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain YA [auth D]	HA [auth B], TA [auth C], U [auth A], YA [auth D]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain HA [auth B] Focus chain TA [auth C] Focus chain U [auth A] Focus chain YA [auth D] Interactions & Density Focus chain HA [auth B] Focus chain TA [auth C] Focus chain U [auth A] Focus chain YA [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C]	FA [auth B], GA [auth B], S [auth A], SA [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain S [auth A] Focus chain SA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain S [auth A] Focus chain SA [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain T [auth A] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] I [auth A] J [auth A] JA [auth C] AA [auth B], BA [auth B], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], T [auth A], UA [auth D], VA [auth D], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain IA [auth C] SDF format, chain V [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain V [auth B]	E [auth A], F [auth A], G [auth A], IA [auth C], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain IA [auth C] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain IA [auth C] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain WA [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth D]	OA [auth C] P [auth A] PA [auth C] Q [auth A] R [auth A] OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], WA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain WA [auth D] Interactions & Density Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain WA [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B]	X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain W [auth B] SDF format, chain XA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth D]	CA [auth B] DA [auth B] EA [auth B] QA [auth C] RA [auth C] CA [auth B], DA [auth B], EA [auth B], QA [auth C], RA [auth C], W [auth B], XA [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain W [auth B] Focus chain XA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain W [auth B] Focus chain XA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M34H5F

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.373	α = 90
b = 61.705	β = 118.04
c = 103.626	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: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description