3LYS | pdb_00003lys

Crystal Structure of the N-terminal domain of the Prophage pi2 protein 01 (integrase) from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR124F

PDB DOI: https://doi.org/10.2210/pdb3LYS/pdb

Classification: RECOMBINATION
Organism(s): Lactococcus lactis subsp. lactis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-02-28 Released: 2010-03-16
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Belote, R.L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.290 (Depositor), 0.279 (DCC)
R-Value Work:
0.260 (Depositor), 0.253 (DCC)
R-Value Observed:
0.260 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target KR124F

Forouhar, F., Abashidze, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Belote, R.L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 80.66 kDa
Atom Count: 5,239
Modeled Residue Count: 629
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prophage pi2 protein 01, integrase	A, B, C, D, E A, B, C, D, E, F	112	Lactococcus lactis subsp. lactis	Mutation(s): 1 Gene Names: int, L364, L36404, LL1008, pi201
UniProt
Find proteins for Q9CGT4 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CGT4 Go to UniProtKB: Q9CGT4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CGT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.290 (Depositor), 0.279 (DCC)
R-Value Work: 0.260 (Depositor), 0.253 (DCC)
R-Value Observed: 0.260 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.704	α = 90
b = 90.272	β = 90
c = 156.948	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2021-10-13
Changes: Database references
Version 1.5: 2024-11-06
Changes: Data collection, Structure summary