4R7O

Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus anthraci

PDB DOI: https://doi.org/10.2210/pdb4R7O/pdb

Classification: HYDROLASE
Organism(s): Bacillus anthracis str. Ames
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-28 Released: 2014-09-10
Deposition Author(s): Kim, Y., Zhou, M., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.204
R-Value Work: 0.154
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus anthraci

Kim, Y., Zhou, M., Shatsman, S., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphoryl diester phosphodiesterase, putative	A, B, C, D, E, F, G A, B, C, D, E, F, G	292	Bacillus anthracis str. Ames	Mutation(s): 0 Gene Names: BA_3560, BAS3300, GBAA_3560
UniProt
Find proteins for A0A6L7H2E6 (Bacillus anthracis) Explore A0A6L7H2E6 Go to UniProtKB: A0A6L7H2E6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L7H2E6
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain T [auth C] MOL2 format, chain DA [auth E] MOL2 format, chain T [auth C]	DA [auth E], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	EA [auth E], HA [auth G], I [auth A], J [auth A], M [auth A], EA [auth E], HA [auth G], I [auth A], J [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], U [auth C], V [auth C], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain X [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain X [auth D]	CA [auth E], L [auth A], P [auth B], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth G] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D]	AA [auth E], BA [auth E], FA [auth F], GA [auth G], H [auth A], AA [auth E], BA [auth E], FA [auth F], GA [auth G], H [auth A], O [auth B], S [auth C], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.204
R-Value Work: 0.154
R-Value Observed: 0.155
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/M34R7O

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.644	α = 90
b = 85.891	β = 121.33
c = 191.539	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing