5JD4 | pdb_00005jd4

Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain

PDB DOI: https://doi.org/10.2210/pdb5JD4/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-04-15 Released: 2016-05-04
Deposition Author(s): Stogios, P.J., Xu, X., Alcaide, M., Yim, V., Cui, H., Martinez-Martinez, M., Ferrer, M., Savchenko, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.211 (Depositor), 0.211 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain

Martinez-Martinez, M.

To be published.

Macromolecule Content

Total Structure Weight: 297.71 kDa
Atom Count: 22,038
Modeled Residue Count: 2,536
Deposited Residue Count: 2,688
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LAE6	A, B, C, D, E A, B, C, D, E, F, G, H	336	uncultured bacterium	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain KB [auth H] SDF format, chain KA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain KB [auth H] MOL2 format, chain KA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain KB [auth H] mmCIF format, chain KA [auth D]	KA [auth D], KB [auth H], N [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain KA [auth D] Focus chain KB [auth H] Focus chain N [auth A] Interactions & Density Focus chain KA [auth D] Focus chain KB [auth H] Focus chain N [auth A]
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain WA [auth F] SDF format, chain W [auth B] SDF format, chain RA [auth E] SDF format, chain O [auth A] SDF format, chain LB [auth H] SDF format, chain LA [auth D] SDF format, chain FB [auth G] SDF format, chain CA [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain LB [auth H] MOL2 format, chain LA [auth D] MOL2 format, chain FB [auth G] MOL2 format, chain CA [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain LB [auth H] mmCIF format, chain LA [auth D] mmCIF format, chain FB [auth G] mmCIF format, chain CA [auth C]	CA [auth C] FB [auth G] LA [auth D] LB [auth H] O [auth A] CA [auth C], FB [auth G], LA [auth D], LB [auth H], O [auth A], RA [auth E], W [auth B], WA [auth F]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain FB [auth G] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain O [auth A] Focus chain RA [auth E] Focus chain W [auth B] Focus chain WA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain FB [auth G] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain O [auth A] Focus chain RA [auth E] Focus chain W [auth B] Focus chain WA [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain XA [auth G] SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HB [auth H] SDF format, chain GB [auth H] SDF format, chain DA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth H] MOL2 format, chain GB [auth H] MOL2 format, chain DA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth G] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth H] mmCIF format, chain GB [auth H] mmCIF format, chain DA [auth D]	DA [auth D] GB [auth H] HB [auth H] I [auth A] J [auth A] DA [auth D], GB [auth H], HB [auth H], I [auth A], J [auth A], P [auth B], Q [auth B], X [auth C], XA [auth G], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth D] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain XA [auth G] Focus chain Y [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain Z [auth C] SDF format, chain YA [auth G] SDF format, chain V [auth B] SDF format, chain UA [auth F] SDF format, chain U [auth B] SDF format, chain TA [auth F] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain R [auth B] SDF format, chain QA [auth E] SDF format, chain PA [auth E] SDF format, chain OA [auth E] SDF format, chain NA [auth E] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain JB [auth H] SDF format, chain IB [auth H] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain EB [auth G] SDF format, chain EA [auth D] SDF format, chain DB [auth G] SDF format, chain CB [auth G] SDF format, chain BB [auth G] SDF format, chain AA [auth C] MOL2 format, chain ZA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth H] MOL2 format, chain IB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain EB [auth G] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth G] MOL2 format, chain CB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain AA [auth C] mmCIF format, chain ZA [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth H] mmCIF format, chain IB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain EB [auth G] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth G] mmCIF format, chain CB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain AA [auth C]	AA [auth C] BB [auth G] CB [auth G] DB [auth G] EA [auth D] AA [auth C], BB [auth G], CB [auth G], DB [auth G], EA [auth D], EB [auth G], GA [auth D], HA [auth D], IA [auth D], IB [auth H], JB [auth H], K [auth A], M [auth A], NA [auth E], OA [auth E], PA [auth E], QA [auth E], R [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], YA [auth G], Z [auth C], ZA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EA [auth D] Focus chain EB [auth G] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain K [auth A] Focus chain M [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EA [auth D] Focus chain EB [auth G] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain K [auth A] Focus chain M [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain VA [auth F] SDF format, chain S [auth B] SDF format, chain MA [auth E] SDF format, chain L [auth A] SDF format, chain JA [auth D] SDF format, chain FA [auth D] SDF format, chain BA [auth C] SDF format, chain AB [auth G] MOL2 format, chain VA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain MA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth G] mmCIF format, chain VA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain MA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth G]	AB [auth G] BA [auth C] FA [auth D] JA [auth D] L [auth A] AB [auth G], BA [auth C], FA [auth D], JA [auth D], L [auth A], MA [auth E], S [auth B], VA [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth G] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain MA [auth E] Focus chain S [auth B] Focus chain VA [auth F] Interactions & Density Focus chain AB [auth G] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain MA [auth E] Focus chain S [auth B] Focus chain VA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.211 (Depositor), 0.211 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.275	α = 68.02
b = 90.098	β = 79.6
c = 110.76	γ = 67.57

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
PHENIX	model building
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Martinez-Martinez, M.

Ferrer, M.

Savchenko, A.

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2017-04-26
Changes: Atomic model, Structure summary
Version 2.0: 2021-08-04
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description