8IK1 | pdb_00008ik1

EstL5 in complex of PMSF

PDB DOI: https://doi.org/10.2210/pdb8IK1/pdb

Classification: HYDROLASE
Organism(s): Geobacillus sp. PA-3
Expression System: Escherichia
Mutation(s): No

Deposited: 2023-02-28 Released: 2023-03-29
Deposition Author(s): Chen, R., Zhang, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.250 (Depositor), 0.249 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

EstL5 in complex of PMSF

Chen, R., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 52.02 kDa
Atom Count: 3,287
Modeled Residue Count: 412
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL family lipase	A, B	230	Geobacillus sp. PA-3	Mutation(s): 0 Gene Names: GEPA3_1571

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ (Subject of Investigation/LOI) Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEB Query on SEB	A, B	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₅ S		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.250 (Depositor), 0.249 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.153	α = 90
b = 105.153	β = 90
c = 128.001	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0907702

Revision History (Full details and data files)

Version 1.0: 2023-03-29
Type: Initial release
Version 2.0: 2023-06-21
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.