3BBJ | pdb_00003bbj

CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE II (TFU_2367) FROM THERMOBIFIDA FUSCA YX AT 2.45 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3BBJ/pdb

Classification: HYDROLASE
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-09 Released: 2007-11-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.243 (Depositor), 0.247 (DCC)
R-Value Work:
0.181 (Depositor), 0.186 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative thioesterase II (YP_290423.1) from Thermobifida fusca YX at 2.45 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 60.52 kDa
Atom Count: 4,281
Modeled Residue Count: 534
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thioesterase II	A, B	272	Thermobifida fusca YX	Mutation(s): 0 Gene Names: YP_290423.1, Tfu_2367
UniProt
Find proteins for Q47MC2 (Thermobifida fusca (strain YX)) Explore Q47MC2 Go to UniProtKB: Q47MC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q47MC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	D [auth A], E [auth A], F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.243 (Depositor), 0.247 (DCC)
R-Value Work: 0.181 (Depositor), 0.186 (DCC)
R-Value Observed: 0.184 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.818	α = 90
b = 103.654	β = 90
c = 54.734	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-09
Changes: Data collection, Refinement description, Structure summary

3BBJ | pdb_00003bbj

CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE II (TFU_2367) FROM THERMOBIFIDA FUSCA YX AT 2.45 A RESOLUTION

Literature

Crystal structure of putative thioesterase II (YP_290423.1) from Thermobifida fusca YX at 2.45 A resolution

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand