3O4P

DFPase at 0.85 Angstrom resolution (H atoms included)

PDB DOI: https://doi.org/10.2210/pdb3O4P/pdb

Classification: HYDROLASE
Organism(s): Loligo vulgaris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-27 Released: 2011-08-17
Deposition Author(s): Liebschner, D., Elias, M., Koepke, J., Lecomte, C., Guillot, B., Jelsch, C., Chabriere, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.85 Å
R-Value Free: 0.121
R-Value Work: 0.103

wwPDB Validation 3D Report Full Report

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

Literature

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase.

Elias, M., Liebschner, D., Koepke, J., Lecomte, C., Guillot, B., Jelsch, C., Chabriere, E.

(2013) BMC Res Notes 6: 308-308

PubMed: 23915572 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1756-0500-6-308
Primary Citation of Related Structures:
3O4P

PubMed Abstract:
Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms.

Organizational Affiliation

Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel.

Macromolecule Content

Total Structure Weight: 37.27 kDa
Atom Count: 3,274
Modelled Residue Count: 314
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diisopropyl-fluorophosphatase	A	314	Loligo vulgaris	Mutation(s): 0 EC: 3.1.8.2
UniProt
Find proteins for Q7SIG4 (Loligo vulgaris) Explore Q7SIG4 Go to UniProtKB: Q7SIG4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SIG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	N [auth A], O [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
ME2 Query on ME2 Download Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A]	V [auth A]	1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE C₇ H₁₆ O₃ CNJRPYFBORAQAU-UHFFFAOYSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A]	T [auth A], U [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain T [auth A] Focus chain U [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
DXE Query on DXE Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	P [auth A], Q [auth A]	1,2-DIMETHOXYETHANE C₄ H₁₀ O₂ XTHFKEDIFFGKHM-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A]
MXE Query on MXE Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	R [auth A], S [auth A]	2-METHOXYETHANOL C₃ H₈ O₂ XNWFRZJHXBZDAG-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain R [auth A] Focus chain S [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A]	W [auth A], X [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain W [auth A] Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.85 Å
R-Value Free: 0.121
R-Value Work: 0.103
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.114	α = 90
b = 81.849	β = 90
c = 86.467	γ = 90

Software Package:

Software Name	Purpose
MoPro	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-17
Type: Initial release
Version 1.1: 2013-08-14
Changes: Database references
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-04-03
Changes: Refinement description