3G7N | pdb_00003g7n

Crystal Structure of a Triacylglycerol Lipase from Penicillium Expansum at 1.3

PDB DOI: https://doi.org/10.2210/pdb3G7N/pdb

Classification: HYDROLASE
Organism(s): Penicillium expansum
Expression System: Komagataella pastoris
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2009-02-10 Released: 2010-02-23
Deposition Author(s): Bian, C.B., Yuan, C., Chen, L.Q., Edward, J.M., Lin, L., Jiang, L.G., Huang, Z.X., Huang, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.208 (Depositor), 0.203 (DCC)
R-Value Work:
0.188 (Depositor), 0.185 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a triacylglycerol lipase from Penicillium expansum at 1.3 A determined by sulfur SAD

Bian, C.B., Yuan, C., Chen, L.Q., Meehan, E.J., Jiang, L.G., Huang, Z.X., Lin, L., Huang, M.D.

(2010) Proteins 78: 1601-1605

PubMed: 20146362 Search on PubMed
DOI: https://doi.org/10.1002/prot.22676
Primary Citation Related Structures:
3G7N

Organizational Affiliation

Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.

Macromolecule Content

Total Structure Weight: 55.88 kDa
Atom Count: 4,260
Modeled Residue Count: 511
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B	258	Penicillium expansum	Mutation(s): 0 Gene Names: PEL EC: 3.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for Q7LST4 (Penicillium expansum) Explore Q7LST4 Go to UniProtKB: Q7LST4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7LST4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A], D [auth A], E [auth A], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.208 (Depositor), 0.203 (DCC)
R-Value Work: 0.188 (Depositor), 0.185 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.27	α = 90
b = 88.27	β = 90
c = 126.616	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-02-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-01-29
Changes: Database references
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

3G7N | pdb_00003g7n

Crystal Structure of a Triacylglycerol Lipase from Penicillium Expansum at 1.3

Literature

Crystal structure of a triacylglycerol lipase from Penicillium expansum at 1.3 A determined by sulfur SAD

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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