6AN9 | pdb_00006an9

Crystal structure of PPk2 class III in complex with ADP from Cytophaga hutchinsonii ATCC 33406

PDB DOI: https://doi.org/10.2210/pdb6AN9/pdb

Classification: TRANSFERASE
Organism(s): Cytophaga hutchinsonii ATCC 33406
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2017-08-12 Released: 2019-01-16
Deposition Author(s): Nocek, B., Joachimiak, A., Yakunin, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Nocek, B., Khusnutdinova, A.N., Ruszkowski, M., Flick, R., Burda, M., Batyrova, K., Brown, G., Mucha, A., Joachimiak, A., Berlicki, L., Yakunin, A.F.

(2018) ACS Catal 8: 10746-10760

DOI: https://doi.org/10.1021/acscatal.8b03151

Macromolecule Content

Total Structure Weight: 35.82 kDa
Atom Count: 2,574
Modeled Residue Count: 296
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphosphate:AMP phosphotransferase	A	305	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0 Gene Names: CHU_0107 EC: 2.7.4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.121	α = 90
b = 111.121	β = 90
c = 178.562	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2020-07-29
Changes: Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description

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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.