3PNZ | pdb_00003pnz

Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes

PDB DOI: https://doi.org/10.2210/pdb3PNZ/pdb

Classification: HYDROLASE
Organism(s): Listeria monocytogenes serotype 4b str. H7858
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-20 Released: 2011-11-23
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.198 (Depositor), 0.190 (DCC)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes

Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 229.68 kDa
Atom Count: 17,578
Modeled Residue Count: 1,970
Deposited Residue Count: 1,980
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase family protein	A, B, C, D, E A, B, C, D, E, F	330	Listeria monocytogenes serotype 4b str. H7858	Mutation(s): 0 Gene Names: LMOh7858_2908

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth E] SDF format, chain YA [auth E] SDF format, chain XA [auth E] SDF format, chain WA [auth E] SDF format, chain VA [auth E] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain HB [auth F] SDF format, chain GB [auth F] SDF format, chain GA [auth C] SDF format, chain FB [auth F] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] MOL2 format, chain ZA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain ZA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain HB [auth F] mmCIF format, chain GB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C]	DA [auth C] EA [auth C] FA [auth C] FB [auth F] GA [auth C] DA [auth C], EA [auth C], FA [auth C], FB [auth F], GA [auth C], GB [auth F], HB [auth F], K [auth A], L [auth A], M [auth A], MA [auth D], NA [auth D], OA [auth D], S [auth B], T [auth B], U [auth B], VA [auth E], WA [auth E], XA [auth E], YA [auth E], ZA [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain SA [auth E] SDF format, chain RA [auth E] SDF format, chain QA [auth E] SDF format, chain PA [auth E] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain JA [auth D] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain CB [auth F] SDF format, chain BB [auth F] SDF format, chain AB [auth F] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain SA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain CB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain SA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain CB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth F] BB [auth F] CB [auth F] G [auth A] AA [auth C], AB [auth F], BB [auth F], CB [auth F], G [auth A], H [auth A], HA [auth D], IA [auth D], JA [auth D], N [auth B], O [auth B], P [auth B], PA [auth E], QA [auth E], RA [auth E], SA [auth E], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain UA [auth E] SDF format, chain TA [auth E] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain LA [auth D] SDF format, chain KA [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain EB [auth F] SDF format, chain DB [auth F] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain UA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain EB [auth F] MOL2 format, chain DB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain UA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain EB [auth F] mmCIF format, chain DB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] DB [auth F] EB [auth F] I [auth A] BA [auth C], CA [auth C], DB [auth F], EB [auth F], I [auth A], J [auth A], KA [auth D], LA [auth D], Q [auth B], R [auth B], TA [auth E], UA [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain UA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain UA [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198 (Depositor), 0.190 (DCC)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.723	α = 90
b = 62.933	β = 89.97
c = 152.744	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-23
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary