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

Starting Model: experimental
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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] mmCIF format, chain HA [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF 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] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain S [auth A] mmCIF 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] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain Y [auth B] mmCIF 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] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth C] mmCIF 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] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF 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] mmCIF 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] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain W [auth B] mmCIF 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] mmCIF 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