4RQ9 | pdb_00004rq9

Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state

PDB DOI: https://doi.org/10.2210/pdb4RQ9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Stigmatella aurantiaca DW4/3-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-10-31 Released: 2016-05-11
Deposition Author(s): Woitowich, N.C., Halavaty, A.S., Gallagher, K.D., Nugent, A.C., Patel, H., Duong, P., Kovaleva, S.E., St.Peter, S., Ozarowski, W.B., Hernandez, C.N., Stojkovic, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.155 (Depositor), 0.160 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state

Woitowich, N.C., Halavaty, A.S., Gallagher, K.D., Nugent, A.C., Patel, H., Duong, P., Kovaleva, S.E., St.Peter, S., Ozarowski, W.B., Hernandez, C.N., Stojkovic, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 41.03 kDa
Atom Count: 2,802
Modelled Residue Count: 304
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoreceptor-histidine kinase BphP	A	348	Stigmatella aurantiaca DW4/3-1	Mutation(s): 1 Gene Names: STAUR_8015, STIAU_3396 EC: 2.7.13.3
UniProt
Find proteins for Q097N3 (Stigmatella aurantiaca (strain DW4/3-1)) Explore Q097N3 Go to UniProtKB: Q097N3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q097N3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA Query on BLA 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]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SRT Query on SRT 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]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.155 (Depositor), 0.160 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.813	α = 90
b = 131.813	β = 90
c = 97.218	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-05-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-11
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2018-01-31
Changes: Database references, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description