3CXA | pdb_00003cxa

Crystal structure of the complex of peptidoglycan recognition protein with alpha-D-glucopyranosyl alpha-D-glucopyranoside at 3.4 A resolution

PDB DOI: https://doi.org/10.2210/pdb3CXA/pdb

Classification: ANTIBIOTIC
Organism(s): Camelus dromedarius
Mutation(s): No

Deposited: 2008-04-24 Released: 2008-05-20
Deposition Author(s): Balaji, K., Sharma, P., Singh, N., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.263 (Depositor), 0.252 (DCC)
R-Value Work:
0.225 (Depositor), 0.222 (DCC)
R-Value Observed:
0.233 (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 peptidoglycan recognition protein with alpha-D-glucopyranosyl alpha-D-glucopyranoside at 3.4 A resolution

Balaji, K., Sharma, P., Singh, N., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 76.88 kDa
Atom Count: 5,400
Modeled Residue Count: 684
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein	A, B, C, D	171	Camelus dromedarius	Mutation(s): 0
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12 Go to UniProtKB: Q9GK12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GK12
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	E, F	2		N/A	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]

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	E, F	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.263 (Depositor), 0.252 (DCC)
R-Value Work: 0.225 (Depositor), 0.222 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.64	α = 90
b = 102.39	β = 90
c = 163.74	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
CNS	refinement
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-20
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: 2024-11-20
Changes: Structure summary