1RLJ

Structural Genomics, a Flavoprotein NrdI from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1RLJ/pdb

Classification: Structural Genomics, unknown function
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2003-11-25 Released: 2004-07-13
Deposition Author(s): Wu, R., Zhang, R., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217
R-Value Work: 0.192
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

1.5A crystal structure of a thioredoxin-like protein NrdI from Bacillus subtilis

Wu, R., Zhang, R., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.4 kDa
Atom Count: 1,239
Modelled Residue Count: 135
Deposited Residue Count: 139
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NrdI protein	A	139	Bacillus subtilis	Mutation(s): 0 Gene Names: NRDI, BSU17370
UniProt
Find proteins for P50618 (Bacillus subtilis (strain 168)) Explore P50618 Go to UniProtKB: P50618
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN 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]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217
R-Value Work: 0.192
R-Value Observed: 0.192
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.236	α = 90
b = 85.236	β = 90
c = 59.992	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-07-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2004-07-13
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

1RLJ

Structural Genomics, a Flavoprotein NrdI from Bacillus subtilis

1.5A crystal structure of a thioredoxin-like protein NrdI from Bacillus subtilis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)