7W1N | pdb_00007w1n

Complex structure of a leaf-branch compost cutinase variant LCC ICCG_KRP

PDB DOI: https://doi.org/10.2210/pdb7W1N/pdb

Classification: HYDROLASE
Organism(s): unidentified prokaryotic organism
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-11-19 Released: 2022-03-09
Deposition Author(s): Niu, D., Zeng, W., Huang, J.W., Chen, C.C., Liu, W.D., Guo, R.T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.165 (Depositor), 0.170 (DCC)
R-Value Work:
0.137 (Depositor), 0.142 (DCC)
R-Value Observed:
0.139 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Substrate-Binding Mode of a Thermophilic PET Hydrolase and Engineering the Enzyme to Enhance the Hydrolytic Efficacy.

Zeng, W., Li, X., Yang, Y., Min, J., Huang, J.-W., Liu, W., Niu, D., Yang, X., Han, X., Zhang, L., Dai, L., Chen, C.-C., Guo, R.-T.

(2022) ACS Catal 12: 3033-3040

DOI: https://doi.org/10.1021/acscatal.1c05800

Macromolecule Content

Total Structure Weight: 28.82 kDa
Atom Count: 2,301
Modeled Residue Count: 258
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leaf-branch compost cutinase	A	270	unidentified prokaryotic organism	Mutation(s): 7 EC: 3.1.1.74 (PDB Primary Data), 3.1.1.101 (PDB Primary Data)
UniProt
Find proteins for G9BY57 (Unknown prokaryotic organism) Explore G9BY57 Go to UniProtKB: G9BY57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G9BY57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCN Query on BCN 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]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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: 1.88 Å
R-Value Free: 0.165 (Depositor), 0.170 (DCC)
R-Value Work: 0.137 (Depositor), 0.142 (DCC)
R-Value Observed: 0.139 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.307	α = 90
b = 60.442	β = 90
c = 81.947	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
SAINT	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-03-09
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: 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.