6K53 | pdb_00006k53

A variant of metagenome-derived GH6 cellobiohydrolase, HmCel6A (P88S/L230F/F414S)

PDB DOI: https://doi.org/10.2210/pdb6K53/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-28 Released: 2020-06-03
Deposition Author(s): Baba, S., Takeda, M., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.160 (Depositor), 0.161 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from a hot spring metagenomic data

Takeda, M., Baba, S., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

To be published.

Macromolecule Content

Total Structure Weight: 47.07 kDa
Atom Count: 4,047
Modeled Residue Count: 428
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH6 cellobiohydrolase, HMCEL6A	A	428	metagenome	Mutation(s): 0 EC: 3.2.1.91

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC 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]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
LI Query on LI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.189 (Depositor), 0.189 (DCC)
R-Value Work: 0.160 (Depositor), 0.161 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.885	α = 90
b = 141.885	β = 90
c = 224.099	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary