4RKR | pdb_00004rkr

Crystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007, complex with lactose

PDB DOI: https://doi.org/10.2210/pdb4RKR/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Arthrobacter sp. FB24
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-13 Released: 2014-11-12
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.252 (Depositor), 0.251 (DCC)
R-Value Work:
0.171 (Depositor), 0.179 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal Structure of LacI Transcriptional Regulator PurR from Arthrobacter Sp, Target Nysgxrc 11027R

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 125.28 kDa
Atom Count: 8,508
Modeled Residue Count: 1,082
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A, B, C, D	294	Arthrobacter sp. FB24	Mutation(s): 0 Gene Names: Arth_3918
UniProt
Find proteins for A0ACD6B8D2 (Arthrobacter sp. (strain FB24)) Explore A0ACD6B8D2 Go to UniProtKB: A0ACD6B8D2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8D2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	E, F, G, H	2		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G88362QR GlyCosmos: G88362QR GlyGen: G88362QR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008 Query on PRD_900008	E, F, G, H	alpha-lactose	Oligosaccharide / Nutrient		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252 (Depositor), 0.251 (DCC)
R-Value Work: 0.171 (Depositor), 0.179 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.936	α = 90
b = 124.912	β = 96.51
c = 117.043	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2014-11-19
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2018-01-31
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-02-10
Changes: Database references, Structure summary
Version 2.2: 2023-09-20
Changes: Data collection, Database references, Refinement description