7CYY | pdb_00007cyy

Crystal structure of Arabinose isomerase from hybrid AI8 with Adonitol

PDB DOI: https://doi.org/10.2210/pdb7CYY/pdb

Classification: ISOMERASE
Organism(s): Geobacillus kaustophilus HTA426, Alicyclobacillus sp. TP7, Alicyclobacillus acidocaldarius subsp. acidocaldarius
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-09-05 Released: 2021-09-08
Deposition Author(s): Hoang, N.K.Q., Dhanasingh, I., Cao, T.P., Sung, J.Y., Shin, S.M., Lee, D.W., Lee, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.261 (Depositor), 0.263 (DCC)
R-Value Work:
0.186 (Depositor), 0.189 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Arabinose isomerase from hyper thermophilic hybrid AI8 with Adonitol

Hoang, N.K.Q., Dhanasingh, I., Cao, T.P., Sung, J.Y., Shin, S.M., Lee, D.W., Lee, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 337.33 kDa
Atom Count: 23,776
Modeled Residue Count: 2,962
Deposited Residue Count: 2,982
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-arabinose isomerase	A, B, C, D, E A, B, C, D, E, F	497	Geobacillus kaustophilus HTA426, Alicyclobacillus sp. TP7, Alicyclobacillus acidocaldarius subsp. acidocaldarius	Mutation(s): 0 Gene Names: araA, GK1904 EC: 5.3.1.4
UniProt
Find proteins for K0IGW6 (Alicyclobacillus sp. TP7) Explore K0IGW6 Go to UniProtKB: K0IGW6
Find proteins for Q2VMT2 (Alicyclobacillus acidocaldarius subsp. acidocaldarius) Explore Q2VMT2 Go to UniProtKB: Q2VMT2
Find proteins for Q5KYP7 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KYP7 Go to UniProtKB: Q5KYP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q5KYP7 K0IGW6 Q2VMT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RB0 (Subject of Investigation/LOI) Query on RB0 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F]	J [auth B] O [auth D] P [auth D] S [auth E] U [auth F] J [auth B], O [auth D], P [auth D], S [auth E], U [auth F], V [auth F]	D-ribitol C₅ H₁₂ O₅ HEBKCHPVOIAQTA-ZXFHETKHSA-N		Interactions Focus chain J [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain J [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C]	G [auth A], M [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	H [auth A] I [auth A] K [auth B] L [auth B] N [auth C] H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], Q [auth D], R [auth D], T [auth E], W [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F]