4XE8 | pdb_00004xe8

Bacillus thuringiensis ParM with ADP

PDB DOI: https://doi.org/10.2210/pdb4XE8/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Bacillus thuringiensis serovar kurstaki str. YBT-1520
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-12-23 Released: 2016-03-16
Deposition Author(s): Jiang, S.M., Robinson, R.C.
Funding Organization(s): Agency for Science, Technology and Research (A*STAR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.275 (Depositor), 0.221 (DCC)
R-Value Work:
0.218 (Depositor), 0.225 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4XE8

Ligand Structure Quality Assessment

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

Literature

A novel plasmid-segregating actin-like protein from Bacillus thuringiensis forms dynamically unstable tubules

Jiang, S.M., Narita, A., Popp, D., Ghoshdastider, U., Lee, L.J., Srinivasan, R., Balasubramanian, M.K., Oda, T., Koh, F.J., Larsson, M., Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 47.93 kDa
Atom Count: 2,974
Modeled Residue Count: 358
Deposited Residue Count: 423
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	423	Bacillus thuringiensis serovar kurstaki str. YBT-1520	Mutation(s): 2 Gene Names: YBT1520_33546
UniProt
Find proteins for A0A140UH76 (Bacillus thuringiensis serovar kurstaki str. YBT-1520) Explore A0A140UH76 Go to UniProtKB: A0A140UH76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A140UH76
Sequence Annotations Expand
Reference Sequence

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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.38 Å
R-Value Free: 0.275 (Depositor), 0.221 (DCC)
R-Value Work: 0.218 (Depositor), 0.225 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.657	α = 90
b = 73.032	β = 90
c = 114.269	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Agency for Science, Technology and Research (A*STAR)	Singapore	12302FG012

Revision History (Full details and data files)

Version 1.0: 2016-03-16
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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