4R7O | pdb_00004r7o

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 (Depositor), 0.204 (DCC)
R-Value Work:
0.154 (Depositor), 0.156 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 237.59 kDa
Atom Count: 16,503
Modeled Residue Count: 1,934
Deposited Residue Count: 2,044
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphoryl diester phosphodiesterase, putative	A, B, C, D, E 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L7H2E6
Sequence Annotations 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] mmCIF format, chain DA [auth E] mmCIF format, chain T [auth C]	DA [auth E], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain T [auth C] Interactions & Density Focus chain DA [auth E] Focus chain T [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain HA [auth G] 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 V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain I [auth A] MOL2 format, chain EA [auth E] MOL2 format, chain HA [auth G] 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 V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain I [auth A] mmCIF format, chain EA [auth E] mmCIF format, chain HA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain I [auth A]	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		Interactions Focus chain EA [auth E] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
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] mmCIF format, chain CA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain X [auth D]	CA [auth E], L [auth A], P [auth B], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain L [auth A] Focus chain P [auth B] Focus chain X [auth D] Interactions & Density Focus chain CA [auth E] Focus chain L [auth A] Focus chain P [auth B] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [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] SDF format, chain BA [auth E] MOL2 format, chain AA [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] MOL2 format, chain BA [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain BA [auth E]	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		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain H [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain H [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.204 (Depositor), 0.204 (DCC)
R-Value Work: 0.154 (Depositor), 0.156 (DCC)
R-Value Observed: 0.155 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description