2QF8 | pdb_00002qf8

Crystal structure of the complex of Buffalo Secretory Glycoprotein with tetrasaccharide at 2.8A resolution

PDB DOI: https://doi.org/10.2210/pdb2QF8/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bubalus bubalis
Mutation(s): No

Deposited: 2007-06-27 Released: 2007-07-10
Deposition Author(s): Singh, A.K., Jain, R., Sinha, M., Kumar, A., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.227 (Depositor), 0.225 (DCC)
R-Value Work:
0.187 (Depositor), 0.195 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the complex of Buffalo Secretory Glycoprotein with Tetrasaccharide at 2.8A resolution

Singh, A.K., Jain, R., Sinha, M., Kumar, A., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 41.99 kDa
Atom Count: 3,109
Modeled Residue Count: 361
Deposited Residue Count: 361
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-3-like protein 1	A	361	Bubalus bubalis	Mutation(s): 0
UniProt
Find proteins for Q7YS85 (Bubalus bubalis) Explore Q7YS85 Go to UniProtKB: Q7YS85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7YS85
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.227 (Depositor), 0.225 (DCC)
R-Value Work: 0.187 (Depositor), 0.195 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.87	α = 90
b = 66.499	β = 90
c = 107.126	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-07-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-07-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-04-15
Changes: Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary