5TRX | pdb_00005trx

Room temperature structure of an extradiol ring-cleaving dioxygenase from B.fuscum determined using serial femtosecond crystallography

PDB DOI: https://doi.org/10.2210/pdb5TRX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brevibacterium fuscum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-10-27 Released: 2017-03-22
Deposition Author(s): Kovaleva, E.G., Oberthuer, D., Tolstikova, A., Mariani, V.
Funding Organization(s): SLAC LDRD program

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.232 (Depositor), 0.237 (DCC)
R-Value Work:
0.184 (Depositor), 0.192 (DCC)
R-Value Observed:
0.187 (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

Double-flow focused liquid injector for efficient serial femtosecond crystallography

Oberthuer, D., Knoska, J., Wiedorn, M.O., Beyerlein, K.R., Bushnell, D.A., Kovaleva, E.G., Heymann, M., Gumprecht, L., Kirian, R.A., Barty, A., Mariani, V., Tolstikova, A., Adriano, L., Awel, S., Barthelmess, M., Dorner, K., Xavier, P.L., Yefanov, O., James, D.R., Nelson, G., Wang, D., Calvey, G., Chen, Y., Schmidt, A., Szczepek, M., Frielingsdorf, S., Lenz, O., Snell, E., Robinson, P.J., Sarler, B., Belsak, G., Macek, M., Wilde, F., Aquila, A., Boutet, S., Liang, M., Hunter, M.S., Scheerer, P., Lipscomb, J.D., Weierstall, U., Kornberg, R.D., Spence, J.C.H., Pollack, L., Chapman, H.N., Bajt, S.

(2017) Sci Rep 7: 44628

DOI: https://doi.org/10.1038/srep44628

Macromolecule Content

Total Structure Weight: 167.43 kDa
Atom Count: 12,065
Modeled Residue Count: 1,434
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoprotocatechuate 2,3-dioxygenase	A, B, C, D	365	Brevibacterium fuscum	Mutation(s): 0
UniProt
Find proteins for Q45135 (Brevibacterium fuscum) Explore Q45135 Go to UniProtKB: Q45135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q45135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], L [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.232 (Depositor), 0.237 (DCC)
R-Value Work: 0.184 (Depositor), 0.192 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.57	α = 90
b = 154.86	β = 90
c = 101.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystFEL	data scaling
CrystFEL	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
SLAC LDRD program	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2018-02-14
Changes: Data collection
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description