5XPX | pdb_00005xpx

Structure elucidation of truncated AMS3 lipase from an Antarctic Pseudomonas

PDB DOI: https://doi.org/10.2210/pdb5XPX/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas sp. A3(2015c)
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2017-06-05 Released: 2018-06-20
Deposition Author(s): Rahman, R.N.Z.R.A., Latip, W.
Funding Organization(s): Universiti Putra Malaysia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.277 (Depositor), 0.279 (DCC)
R-Value Work:
0.222 (Depositor), 0.228 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure elucidation of truncated AMS3 lipase from an Antarctic Pseudomonas

Rahman, R.N.Z.R.A., Latip, W.

To be published.

Macromolecule Content

Total Structure Weight: 96.14 kDa
Atom Count: 6,066
Modeled Residue Count: 765
Deposited Residue Count: 858
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B [auth E]	429	Pseudomonas sp. A3(2015c)	Mutation(s): 0 EC: 3.1.1.3
UniProt
Find proteins for A0A0K0PTR1 (Pseudomonas sp. A3(2015c)) Explore A0A0K0PTR1 Go to UniProtKB: A0A0K0PTR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0K0PTR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E SDF format, chain C [auth A] MOL2 format, chain E MOL2 format, chain C [auth A] mmCIF format, chain E mmCIF format, chain C [auth A]	C [auth A], E	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E Interactions & Density Focus chain C [auth A] Focus chain E
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth E] SDF format, chain D [auth A] MOL2 format, chain F [auth E] MOL2 format, chain D [auth A] mmCIF format, chain F [auth E] mmCIF format, chain D [auth A]	D [auth A], F [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth E] Interactions & Density Focus chain D [auth A] Focus chain F [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.277 (Depositor), 0.279 (DCC)
R-Value Work: 0.222 (Depositor), 0.228 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.753	α = 90
b = 94.693	β = 90
c = 126.431	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing
HKL-3000	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Rahman, R.N.Z.R.A.

Funding Organization	Location	Grant Number
Universiti Putra Malaysia	Malaysia	9479200

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.