7R25 | pdb_00007r25

Bacillus pumilus Lipase A

PDB DOI: https://doi.org/10.2210/pdb7R25/pdb

Classification: HYDROLASE
Organism(s): Bacillus pumilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2022-02-04 Released: 2022-05-25
Deposition Author(s): Lund, B.A.
Funding Organization(s): Research Council of Norway

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.87 Å
R-Value Free:
0.133 (Depositor), 0.130 (DCC)
R-Value Work:
0.111 (Depositor), 0.110 (DCC)
R-Value Observed:
0.112 (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

Structure and Mechanism of a Cold-Adapted Bacterial Lipase

Lund, B.A., Svalberg, L., Purg, M., Chukwu, G., Widersten, M., Isaksen, G.V., Brandsdal, B.O., Aqvist, J.

(2022) Biochemistry 61: 933-942

DOI: https://doi.org/10.1021/acs.biochem.2c00087

Macromolecule Content

Total Structure Weight: 20.84 kDa
Atom Count: 1,743
Modeled Residue Count: 184
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	190	Bacillus pumilus	Mutation(s): 0 Gene Names: L5 Membrane Entity: Yes
UniProt
Find proteins for W8FKE7 (Bacillus pumilus) Explore W8FKE7 Go to UniProtKB: W8FKE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8FKE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PPI Query on PPI Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.87 Å
R-Value Free: 0.133 (Depositor), 0.130 (DCC)
R-Value Work: 0.111 (Depositor), 0.110 (DCC)
R-Value Observed: 0.112 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.109	α = 90
b = 54.697	β = 92.72
c = 40.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Council of Norway	Norway	262695
Research Council of Norway	Norway	274858

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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.