5AVN: Xylose isomerase

Name: PDB 5AVN: The 1.03 angstrom structure (P212121) of glucose isomerase crystallized in high-strength agarose hydrogel
Published: 2015-07-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: isomerase

The 1.03 angstrom structure (P212121) of glucose isomerase crystallized in high-strength agarose hydrogel. Determined by X-ray diffraction at 1.03 Å resolution. Released 8 Jul 2015.

Method: X-ray diffraction
Resolution: 1.03 Å
Organism: Streptomyces rubiginosus
Chains: 2
Atoms: 7,812
Mol. weight: 86.88 kDa
Ligands: CA, MN
Released: 8 Jul 2015

Explore 5AVN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AVN contains 45 α-helices and 36 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	11-14	4	1
α-helix	15-18	4
β-strand	24	1	2
β-strand	27	1	2
α-helix	32-35	4
α-helix	36-45	10
β-strand	50-54	5	1
α-helix	55-58	4
α-helix	65-82	18
β-strand	85-90	6	1
α-helix	97-99	3
α-helix	109-129	21
β-strand	133-136	4	1
β-strand	142-143	2	3
α-helix	151-172	22
β-strand	177-180	4	1
β-strand	190-191	2	3
α-helix	196-203	8
α-helix	209-211	3
β-strand	212-214	3	1
β-strand	217	1	1
α-helix	218-222	5
α-helix	228-237	10
β-strand	241	1	1
β-strand	245-246	2	1
β-strand	248	1	4
β-strand	258	1	4
α-helix	259	1
β-strand	260	1	5
β-strand	262	1	5
α-helix	265-278	14
β-strand	284-286	3	1
α-helix	296-322	27
α-helix	324-332	9
α-helix	335-338	4
α-helix	347-352	6
α-helix	354-356	3
α-helix	362-367	6
α-helix	372-383	12

Chain B: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	11-14	4	6
α-helix	15-18	4
β-strand	24	1	7
β-strand	27	1	7
α-helix	32-35	4
α-helix	36-45	10
β-strand	50-54	5	6
α-helix	55-58	4
α-helix	65-82	18
β-strand	85-90	6	6
α-helix	97-99	3
α-helix	109-128	20
β-strand	133-136	4	6
β-strand	142-143	2	8
α-helix	146-148	3
α-helix	151-171	21
β-strand	177-180	4	6
β-strand	190-191	2	8
α-helix	196-203	8
α-helix	209-211	3
β-strand	212-214	3	6
β-strand	217	1	6
α-helix	218-222	5
α-helix	228-237	10
β-strand	241	1	6
β-strand	244-246	3	6
β-strand	248	1	9
β-strand	258	1	9
α-helix	259	1
β-strand	260	1	10
β-strand	262	1	10
α-helix	265-278	14
β-strand	284-286	3	6
α-helix	296-322	27
α-helix	324-332	9
α-helix	335-339	5
α-helix	347-352	6
α-helix	354-356	3
α-helix	362-367	6
α-helix	372-384	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Xylose isomerase	A, B	protein	387	Streptomyces rubiginosus	P24300 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5AVN_1 Xylose isomerase (chains A, B)
NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPF
GSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIR
NIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIE
PKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKL
FHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWA
SAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFD
VDAAAARGMAFERLDQLAMDHLLGARG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
MN	Manganese (II) ion	Mn	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Growth of protein crystals in hydrogels prevents osmotic shock. Sugiyama, S., Maruyama, M., Sazaki, G. et al. J Am Chem Soc (2012) 134:5786-5789. DOI 10.1021/ja301584y · PubMed

Other PDB entries of the same protein (UniProt P24300 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AVH 0.9 Å, The 0.90 angstrom structure (I222) of glucose isomerase crystallized in high-strength…
2GLK 0.94 Å, High-resolution study of D-Xylose isomerase, 0.94A resolution.
4A8I 0.95 Å, Protein crystallization and microgravity: glucose isomerase crystals grown during the…
3U3H 0.97 Å, X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of…
1MNZ 0.99 Å, Atomic structure of Glucose isomerase
7DMM 0.99 Å, Structure of a glucose isomerase crystal grown in an aqueous glycerol solution without…
8WDG 0.99 Å, Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus
6YBO 1.06 Å, RT structure of Glucose Isomerase obtained at 1.06 A resolution from crystal grown in a…
9SO8 1.09 Å, Glucose/ xylose isomerase under 100 MPa
6QRR 1.1 Å, X-ray radiation dose series on xylose isomerase - 0.13 MGy
6QRS 1.17 Å, X-ray radiation dose series on xylose isomerase - 0.13 MGy
6QRT 1.17 Å, X-ray radiation dose series on xylose isomerase - 1.38 MGy

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