7D2W | pdb_00007d2w

Crystal structure of PHIT/PHISTa-like subfamily PF3D7_1372300 protein from plasmodium falciparum

PDB DOI: https://doi.org/10.2210/pdb7D2W/pdb

Classification: PROTEIN BINDING
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-09-17 Released: 2021-09-22
Deposition Author(s): Gao, Y., Yang, B.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7D2W

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

Literature

Structural analysis of binding between Plasmodium falciparum PHIST and the parasite virulence factor PfEMP1 protein

Yang, B.L., Gao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 45.11 kDa
Atom Count: 2,400
Modeled Residue Count: 250
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PRESAN domain-containing protein	A, B	190	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF3D7_1372300
UniProt
Find proteins for A0A143ZZR8 (Plasmodium falciparum (isolate 3D7)) Explore A0A143ZZR8 Go to UniProtKB: A0A143ZZR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A143ZZR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.204 (Depositor), 0.204 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.523	α = 90
b = 78.523	β = 90
c = 100.559	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	No. 21736002, 31770827, 31961133015

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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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.