3LZE | pdb_00003lze

Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37C catalytic residue mutant

PDB DOI: https://doi.org/10.2210/pdb3LZE/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Plasmodium vivax
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-03-01 Released: 2010-04-07
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.220 (Depositor), 0.225 (DCC)
R-Value Work:
0.191 (Depositor), 0.196 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural analysis of the dual-functional 6-pyruvoyltetrahydropterin synthase from Malaria parasites.

Larson, E.T., Bosch, J., Kim, J.E., Kelley, A., Castaneda, L., Napuli, A., Mueller, N., Verlinde, C.L.M.J., Van Voorhis, W.C., Buckner, F.S., Fan, E., Hol, W.G.J., Merritt, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 21.2 kDa
Atom Count: 1,444
Modeled Residue Count: 163
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 6-pyruvoyl tetrahydrobiopterin synthase	A	180	Plasmodium vivax	Mutation(s): 1 Gene Names: PVX_114505 EC: 4.2.3.12
UniProt
Find proteins for A5K2B2 (Plasmodium vivax (strain Salvador I)) Explore A5K2B2 Go to UniProtKB: A5K2B2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K2B2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE0 Query on PE0 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]	PTERINE C₆ H₅ N₅ O HNXQXTQTPAJEJL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.220 (Depositor), 0.225 (DCC)
R-Value Work: 0.191 (Depositor), 0.196 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.495	α = 90
b = 131.495	β = 90
c = 73.67	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-04-07

Deposition Author(s):

Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History (Full details and data files)

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2023-09-06
Changes: Data collection, 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.