3LD1 | pdb_00003ld1

Crystal Structure of IBV Nsp2a

PDB DOI: https://doi.org/10.2210/pdb3LD1/pdb

Classification: HYDROLASE
Organism(s): Avian infectious bronchitis virus (strain M41)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-01-12 Released: 2011-05-25
Deposition Author(s): Xu, Y., Cong, L., Wei, L., Fu, J., Chen, C., Yang, A., Tang, H., Bartlam, M., Rao, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.284 (Depositor), 0.271 (DCC)
R-Value Work:
0.216 (Depositor), 0.208 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LD1

This is version 1.4 of the entry. See complete history.

Literature

IBV nsp2 is an endosome-associated protein and viral pathogenicity factor

Xu, Y., Ye, Z., Wei, L., Cong, L., Fu, J., Chen, C., Yang, A., Wu, W., Tang, H., Bartlam, M., Rao, Z.

To be published.

Macromolecule Content

Total Structure Weight: 39.76 kDa
Atom Count: 2,882
Modeled Residue Count: 359
Deposited Residue Count: 359
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	A	359	Avian infectious bronchitis virus (strain M41)	Mutation(s): 3 Gene Names: 1a, 1ab EC: 3.4.22
UniProt
Find proteins for P0C6V5 (Avian infectious bronchitis virus (strain M41)) Explore P0C6V5 Go to UniProtKB: P0C6V5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6V5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.284 (Depositor), 0.271 (DCC)
R-Value Work: 0.216 (Depositor), 0.208 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.179	α = 90
b = 114.179	β = 90
c = 60.979	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-05-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references
Version 1.4: 2024-02-21
Changes: Data collection