3JYF | pdb_00003jyf

The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

PDB DOI: https://doi.org/10.2210/pdb3JYF/pdb

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

Deposited: 2009-09-21 Released: 2009-09-29
Deposition Author(s): Fan, Y., Volkart, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.231 (Depositor), 0.203 (DCC)
R-Value Work:
0.179 (Depositor)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

Fan, Y., Volkart, L., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 76.69 kDa
Atom Count: 5,817
Modeled Residue Count: 671
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase bifunctional periplasmic protein	A, B	339	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: cpdB, KPN78578_45340, KPN_04607 EC: 3.1.3.6 (UniProt), 3.1.4.16 (UniProt)
UniProt
Find proteins for A6THC4 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6THC4 Go to UniProtKB: A6THC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6THC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth B]	D [auth A], Q [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain Q [auth B]
TAM Query on TAM Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain N [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] M [auth A] F [auth A], G [auth A], H [auth A], I [auth A], M [auth A], N [auth A], S [auth B], T [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain E [auth A]	C [auth A], E [auth A], O [auth B], P [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [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: 2.43 Å
R-Value Free: 0.231 (Depositor), 0.203 (DCC)
R-Value Work: 0.179 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.041	α = 90
b = 106.041	β = 90
c = 182.967	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-09-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary