5EUM | pdb_00005eum

1.8 Angstrom Crystal Structure of ATP-binding Component of Fused Lipid Transporter Subunits of ABC superfamily from Haemophilus influenzae.

PDB DOI: https://doi.org/10.2210/pdb5EUM/pdb

Classification: HYDROLASE
Organism(s): Haemophilus influenzae PittII
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-11-18 Released: 2015-12-02
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.204 (Depositor), 0.235 (DCC)
R-Value Work:
0.171 (Depositor)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

1.8 Angstrom Crystal Structure of ATP-binding Component of Fused Lipid Transporter Subunits of ABC superfamily from Haemophilus influenzae.

Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 58.46 kDa
Atom Count: 4,627
Modeled Residue Count: 499
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid A export ATP-binding/permease protein MsbA	A, B	258	Haemophilus influenzae PittII	Mutation(s): 0 Gene Names: msbA, CGSHiII_09046 EC: 3.6.3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B]	M [auth A], W [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain W [auth B]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	J [auth A] K [auth A] L [auth A] S [auth B] T [auth B] J [auth A], K [auth A], L [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [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 H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], Q [auth B], R [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 H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	C [auth A], D [auth A], O [auth B], P [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ Query on MLZ	A, B	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.204 (Depositor), 0.235 (DCC)
R-Value Work: 0.171 (Depositor)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.237	α = 90
b = 95.237	β = 90
c = 60.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
BLU-MAX	data collection

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-12-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-12-02
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description