4GBG

Crystal structure of Ethyl acetoacetate treated lipase from Thermomyces lanuginosa at 2.9 A resolution

PDB DOI: https://doi.org/10.2210/pdb4GBG/pdb

Classification: HYDROLASE
Organism(s): Thermomyces lanuginosus
Mutation(s): No

Deposited: 2012-07-27 Released: 2012-08-22
Deposition Author(s): Yamini, S., Mukherjee, J., Gupta, M.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.247
R-Value Work: 0.226
R-Value Observed: 0.226

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Ethyl acetoacetate treated lipase from Thermomyces lanuginosa at 2.9 A resolution

Yamini, S., Mukherjee, J., Gupta, M.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 59.26 kDa
Atom Count: 4,527
Modelled Residue Count: 538
Deposited Residue Count: 538
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, B	269	Thermomyces lanuginosus	Mutation(s): 0 EC: 3.1.1.3
UniProt
Find proteins for O59952 (Thermomyces lanuginosus) Explore O59952 Go to UniProtKB: O59952
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O59952
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
EAC Query on EAC 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]	ethyl 3-oxobutanoate C₆ H₁₀ O₃ XYIBRDXRRQCHLP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.247
R-Value Work: 0.226
R-Value Observed: 0.226
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.489	α = 90
b = 140.489	β = 90
c = 80.69	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-22
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-13
Changes: Structure summary

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4GBG

Crystal structure of Ethyl acetoacetate treated lipase from Thermomyces lanuginosa at 2.9 A resolution

Crystal structure of Ethyl acetoacetate treated lipase from Thermomyces lanuginosa at 2.9 A resolution

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)