3B6N | pdb_00003b6n

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase PV003920 from Plasmodium vivax

PDB DOI: https://doi.org/10.2210/pdb3B6N/pdb

Classification: LYASE
Organism(s): Plasmodium vivax Sal-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-29 Released: 2007-11-20
Deposition Author(s): Wernimont, A.K., Lew, J., Kozieradzki, I., Lin, Y.H., Sun, X., Khuu, C., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bochkarev, A., Hui, R., Artz, J.D., Xiao, T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.257 (Depositor), 0.218 (DCC)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase PV003920 from Plasmodium vivax.

Wernimont, A.K., Lew, J., Kozieradzki, I., Lin, Y.H., Sun, X., Khuu, C., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bochkarev, A., Hui, R., Artz, J.D., Xiao, T.

To be published.

Macromolecule Content

Total Structure Weight: 20.28 kDa
Atom Count: 1,179
Modeled Residue Count: 150
Deposited Residue Count: 187
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A	187	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PV003920, PVX_003920 EC: 4.6.1.12
UniProt
Find proteins for A5KBP6 (Plasmodium vivax (strain Salvador I)) Explore A5KBP6 Go to UniProtKB: A5KBP6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5KBP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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: 2.26 Å
R-Value Free: 0.257 (Depositor), 0.218 (DCC)
R-Value Work: 0.204 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.661	α = 90
b = 79.661	β = 90
c = 79.661	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description