9BLD | pdb_00009bld

crystal structure of thermostable dienelactone hydrolase

PDB DOI: https://doi.org/10.2210/pdb9BLD/pdb

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

Deposited: 2024-04-30 Released: 2025-05-14
Deposition Author(s): Muniz, J.R.C., Almeida, D., Brito, V., Ciancaglini, I., Sandano, A.L.H., Squina, F., Garcia, W.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.189 (Depositor), 0.200 (DCC)
R-Value Work:
0.164 (Depositor), 0.176 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

crystal structure of thermostable dienelactone hydrolase

Muniz, J.R.C., Almeida, D., Brito, V., Ciancaglini, I., Sandano, A.L.H., Squina, F., Garcia, W.

To be published.

Macromolecule Content

Total Structure Weight: 109.04 kDa
Atom Count: 8,279
Modeled Residue Count: 935
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxymethylenebutenolidase	A, B, C, D	240	Hydrogenobacter thermophilus	Mutation(s): 0 Gene Names: HTH_1817
UniProt
Find proteins for D3DKA9 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)) Explore D3DKA9 Go to UniProtKB: D3DKA9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3DKA9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.189 (Depositor), 0.200 (DCC)
R-Value Work: 0.164 (Depositor), 0.176 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.385	α = 90
b = 87.298	β = 90
c = 143.245	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2020/15595-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2020/05784-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/05731-2
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/08958-8
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/23279-6
Sao Paulo Research Foundation (FAPESP)	Brazil	2019/19360-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2020/11019-8
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/04254-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/14112-4
Sao Paulo Research Foundation (FAPESP)	Brazil	2023/04782-5
Sao Paulo Research Foundation (FAPESP)	Brazil	2023/04828-5
Sao Paulo Research Foundation (FAPESP)	Brazil	2023/12398-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2023/04941-6
Sao Paulo Research Foundation (FAPESP)	Brazil	2023/08832-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	305816/2020-9
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	422132/2018-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	306279/2020-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	315847/2021-2
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	403844/2023-1
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	176662/2023-5
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	304998/2023-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	307199/2023-1
Other government	Brazil	88887.625460/2021-00
Other government	Brazil	88887.600186/2021-00
Other government	Brazil	88887.518696/2020-00