4ICI | pdb_00004ici

Crystal structure of a putative flavoprotein (BACEGG_01620) from Bacteroides eggerthii DSM 20697 at 1.40 A resolution

PDB DOI: https://doi.org/10.2210/pdb4ICI/pdb

Classification: FLAVOPROTEIN
Organism(s): Bacteroides eggerthii DSM 20697
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-12-10 Released: 2013-01-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.147 (Depositor), 0.158 (DCC)
R-Value Work:
0.115 (Depositor), 0.129 (DCC)
R-Value Observed:
0.116 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of a putative flavoprotein (BACEGG_01620) from Bacteroides eggerthii DSM 20697 at 1.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 19.88 kDa
Atom Count: 1,594
Modeled Residue Count: 159
Deposited Residue Count: 171
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative flavoprotein	A	171	Bacteroides eggerthii DSM 20697	Mutation(s): 0 Gene Names: BACEGG_01620, ZP_03458840.1

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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EPE Query on EPE 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]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
UNL Query on UNL Download:Ideal Coordinates CCD File	C [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.147 (Depositor), 0.158 (DCC)
R-Value Work: 0.115 (Depositor), 0.129 (DCC)
R-Value Observed: 0.116 (Depositor)

Diffraction Data:

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.625	α = 90
b = 85.625	β = 90
c = 58.134	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-01-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-01-02
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-02-01
Changes: Database references, Derived calculations
Version 1.3: 2024-11-06
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.