8SD5 | pdb_00008sd5

Crystal structure of HPPK from Methanocaldococcus jannaschii

PDB DOI: https://doi.org/10.2210/pdb8SD5/pdb

Classification: TRANSFERASE
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-06 Released: 2024-07-03
Deposition Author(s): Shaw, G.X., Needle, D., Stair, N.R., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.290 (Depositor), 0.290 (DCC)
R-Value Work:
0.243 (Depositor), 0.243 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of HPPK from Methanocaldococcus jannaschii

Shaw, G.X., Needle, D., Stair, N.R., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

To be published.

Macromolecule Content

Total Structure Weight: 110.77 kDa
Atom Count: 7,003
Modeled Residue Count: 858
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase	A, B, C, D	241	Methanocaldococcus jannaschii	Mutation(s): 0 Gene Names: mptE, MJ1634 EC: 2.7.6.3
UniProt
Find proteins for Q59028 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q59028 Go to UniProtKB: Q59028
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59028
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.290 (Depositor), 0.290 (DCC)
R-Value Work: 0.243 (Depositor), 0.243 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.729	α = 90
b = 75.744	β = 90
c = 179.578	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History (Full details and data files)

Version 1.0: 2024-07-03
Type: Initial release

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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.