3OIH | pdb_00003oih

Crystal Structure of the complex of xylanase-alpha-amylase inhibitor Protein (XAIP-I) with trehalose at 1.87 A resolution

PDB DOI: https://doi.org/10.2210/pdb3OIH/pdb

Classification: HYDROLASE INHIBITOR
Organism(s): Scadoxus multiflorus
Mutation(s): No

Deposited: 2010-08-19 Released: 2010-09-22
Deposition Author(s): Kumar, M., Kumar, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.211 (Depositor), 0.213 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal Structure of the complex of xylanase-alpha-amylase inhibitor Protein (XAIP-I) with trehalose at 1.87 A resolution

Kumar, M., Kumar, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 30.43 kDa
Atom Count: 2,390
Modeled Residue Count: 272
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haementhin	A	272	Scadoxus multiflorus	Mutation(s): 0 EC: 3.2.1.14
UniProt
Find proteins for B2ZGS7 (Scadoxus multiflorus) Explore B2ZGS7 Go to UniProtKB: B2ZGS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2ZGS7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	B	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.211 (Depositor), 0.213 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.238	α = 90
b = 64.677	β = 102.33
c = 48.852	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary