3U27 | pdb_00003u27

Crystal structure of ethanolamine utilization protein EutL from Leptotrichia buccalis C-1013-b

PDB DOI: https://doi.org/10.2210/pdb3U27/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Leptotrichia buccalis C-1013-b
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-10-01 Released: 2012-02-08
Deposition Author(s): Wu, R., Gu, M., Kerfeld, C.A., Salmeen, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.182 (Depositor), 0.179 (DCC)
R-Value Work:
0.157 (Depositor), 0.155 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of ethanolamine utilization protein EutL from Leptotrichia buccalis C-1013-b

Wu, R., Gu, M., Kerfeld, C.A., Salmeen, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 139.19 kDa
Atom Count: 10,884
Modeled Residue Count: 1,306
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcompartments protein	A [auth C] B [auth A] C [auth B] D E A [auth C], B [auth A], C [auth B], D, E, F	220	Leptotrichia buccalis C-1013-b	Mutation(s): 0 Gene Names: Lebu_0063
UniProt
Find proteins for C7NCS6 (Leptotrichia buccalis (strain ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b)) Explore C7NCS6 Go to UniProtKB: C7NCS6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7NCS6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain S [auth B] SDF format, chain T [auth D] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain S [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain S [auth B] mmCIF format, chain T [auth D] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain H [auth C]	H [auth C] I [auth C] O [auth A] P [auth A] Q [auth A] H [auth C], I [auth C], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth D], U [auth F], V [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth D] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain H [auth C] Focus chain I [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth D] Focus chain U [auth F] Focus chain V [auth F]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain G [auth C] MOL2 format, chain J [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain G [auth C] mmCIF format, chain J [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain G [auth C]	G [auth C], J [auth C], M [auth A], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain J [auth C] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain G [auth C] Focus chain J [auth C] Focus chain M [auth A] Focus chain N [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain R [auth A] SDF format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain R [auth A] MOL2 format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain R [auth A] mmCIF format, chain L [auth C]	K [auth C], L [auth C], R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Focus chain R [auth A] Interactions & Density Focus chain K [auth C] Focus chain L [auth C] Focus chain R [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth C] B [auth A] C [auth B] D E A [auth C], B [auth A], C [auth B], D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.182 (Depositor), 0.179 (DCC)
R-Value Work: 0.157 (Depositor), 0.155 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.854	α = 90
b = 105.644	β = 90.06
c = 101.551	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2012-03-28
Changes: Other
Version 1.2: 2012-04-11
Changes: Database references, Structure summary
Version 1.3: 2012-09-12
Changes: Database references, Structure summary
Version 1.4: 2020-01-29
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary