4RXM | pdb_00004rxm

Crystal structure of periplasmic ABC transporter solute binding protein A7JW62 from Mannheimia haemolytica PHL213, Target EFI-511105, in complex with Myo-inositol

PDB DOI: https://doi.org/10.2210/pdb4RXM/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Mannheimia haemolytica PHL213
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-11 Released: 2014-12-24
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siedel, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.187 (Depositor), 0.212 (DCC)
R-Value Work:
0.156 (Depositor)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of solute binding sugar transporter A7JW62 from Mannheimia haemolytica, Target EFI-511105.

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Morisco, L.L., Wasserman, S.R., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 63.63 kDa
Atom Count: 4,899
Modeled Residue Count: 579
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible sugar ABC superfamily ATP binding cassette transporter, binding protein	A, B	292	Mannheimia haemolytica PHL213	Mutation(s): 0 Gene Names: MHA_2416
UniProt
Find proteins for A0A249A2K7 (Mannheimia haemolytica) Explore A0A249A2K7 Go to UniProtKB: A0A249A2K7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A249A2K7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
INS Query on INS Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C₆ H₁₂ O₆ CDAISMWEOUEBRE-GPIVLXJGSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ASP Query on ASP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.187 (Depositor), 0.212 (DCC)
R-Value Work: 0.156 (Depositor)
R-Value Observed: 0.157 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.784	α = 90
b = 120.175	β = 90
c = 137.741	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Structure summary