5TPI | pdb_00005tpi

1.47 Angstrom Crystal Structure of the C-terminal Substrate Binding Domain of LysR Family Transcriptional Regulator from Klebsiella pneumoniae.

PDB DOI: https://doi.org/10.2210/pdb5TPI/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-10-20 Released: 2016-11-02
Deposition Author(s): Minasov, G., Wawrzak, Z., Sandoval, J., Evdokimova, E., Grimshaw, S., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.181 (Depositor), 0.184 (DCC)
R-Value Work:
0.137 (Depositor), 0.139 (DCC)
R-Value Observed:
0.139 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

1.47 Angstrom Crystal Structure of the C-terminal Substrate Binding Domain of LysR Family Transcriptional Regulator from Klebsiella pneumoniae.

Minasov, G., Wawrzak, Z., Sandoval, J., Evdokimova, E., Grimshaw, S., Kwon, K., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 23.33 kDa
Atom Count: 1,938
Modeled Residue Count: 205
Deposited Residue Count: 211
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator (LysR family)	A	211	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: yneJ, KPN_01634
UniProt
Find proteins for A6T8Z4 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T8Z4 Go to UniProtKB: A6T8Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6T8Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-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]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.181 (Depositor), 0.184 (DCC)
R-Value Work: 0.137 (Depositor), 0.139 (DCC)
R-Value Observed: 0.139 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.756	α = 90
b = 40.228	β = 129.41
c = 68.211	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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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.