3EO8 | pdb_00003eo8

Crystal structure of BluB-like flavoprotein (YP_001089088.1) from CLOSTRIDIUM DIFFICILE 630 at 1.74 A resolution

PDB DOI: https://doi.org/10.2210/pdb3EO8/pdb

Classification: FLAVOPROTEIN
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-26 Released: 2008-11-04
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.198 (Depositor), 0.205 (DCC)
R-Value Work:
0.156 (Depositor), 0.171 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of BluB-like flavoprotein (YP_001089088.1) from CLOSTRIDIUM DIFFICILE 630 at 1.74 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 155.07 kDa
Atom Count: 12,860
Modeled Residue Count: 1,314
Deposited Residue Count: 1,314
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BluB-like flavoprotein	A, B, C, D, E A, B, C, D, E, F	219	Clostridioides difficile 630	Mutation(s): 0 Gene Names: YP_001089088.1, CD2572
UniProt
Find proteins for Q182R2 (Clostridioides difficile (strain 630)) Explore Q182R2 Go to UniProtKB: Q182R2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q182R2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain GA [auth F] MOL2 format, chain AA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain GA [auth F] mmCIF format, chain AA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain GA [auth F]	AA [auth E] G [auth A] GA [auth F] K [auth B] Q [auth C] AA [auth E], G [auth A], GA [auth F], K [auth B], Q [auth C], V [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain AA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain KA [auth F] SDF format, chain FA [auth E] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain FA [auth E] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain KA [auth F] mmCIF format, chain FA [auth E]	FA [auth E] KA [auth F] O [auth B] P [auth B] T [auth C] FA [auth E], KA [auth F], O [auth B], P [auth B], T [auth C], U [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain KA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain KA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Z [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain IA [auth F] SDF format, chain I [auth A] SDF format, chain HA [auth F] SDF format, chain H [auth A] SDF format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain IA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain IA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] DA [auth E] H [auth A] HA [auth F] BA [auth E], CA [auth E], DA [auth E], H [auth A], HA [auth F], I [auth A], IA [auth F], L [auth B], M [auth B], R [auth C], W [auth D], X [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Y [auth D] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain JA [auth F] SDF format, chain EA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain JA [auth F] MOL2 format, chain EA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain JA [auth F] mmCIF format, chain EA [auth E]	EA [auth E] J [auth A] JA [auth F] N [auth B] S [auth C] EA [auth E], J [auth A], JA [auth F], N [auth B], S [auth C], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.198 (Depositor), 0.205 (DCC)
R-Value Work: 0.156 (Depositor), 0.171 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.843	α = 90
b = 183.265	β = 104.89
c = 74.393	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-11-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary