4RK6 | pdb_00004rk6

Crystal structure of LacI family transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926, with bound glucose

PDB DOI: https://doi.org/10.2210/pdb4RK6/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Weissella paramesenteroides ATCC 33313
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-11 Released: 2014-10-29
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., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.198 (Depositor), 0.209 (DCC)
R-Value Work:
0.168 (Depositor), 0.182 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926

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., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 65.44 kDa
Atom Count: 4,718
Modeled Residue Count: 539
Deposited Residue Count: 574
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-resistance amylase regulator	A, B	287	Weissella paramesenteroides ATCC 33313	Mutation(s): 0 Gene Names: ccpA, HMPREF0877_1426
UniProt
Find proteins for C5RBT0 (Weissella paramesenteroides ATCC 33313) Explore C5RBT0 Go to UniProtKB: C5RBT0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5RBT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.198 (Depositor), 0.209 (DCC)
R-Value Work: 0.168 (Depositor), 0.182 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.564	α = 90
b = 102.564	β = 90
c = 128.055	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-29

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-10-29
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Structure summary