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- PDB-3lys: Crystal Structure of the N-terminal domain of the Prophage pi2 pr... -

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Basic information

Entry
Database: PDB / ID: 3lys
TitleCrystal Structure of the N-terminal domain of the Prophage pi2 protein 01 (integrase) from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR124F
ComponentsProphage pi2 protein 01, integrase
KeywordsRECOMBINATION / helical N-terminal domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
: / Tyrosine recombinase, N-terminal domain / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core ...: / Tyrosine recombinase, N-terminal domain / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Prophage pi2 protein 01, integrase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. ...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)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target KR124F
Authors: 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.
History
DepositionFeb 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prophage pi2 protein 01, integrase
B: Prophage pi2 protein 01, integrase
C: Prophage pi2 protein 01, integrase
D: Prophage pi2 protein 01, integrase
E: Prophage pi2 protein 01, integrase
F: Prophage pi2 protein 01, integrase


Theoretical massNumber of molelcules
Total (without water)80,6626
Polymers80,6626
Non-polymers00
Water91951
1
A: Prophage pi2 protein 01, integrase


Theoretical massNumber of molelcules
Total (without water)13,4441
Polymers13,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prophage pi2 protein 01, integrase


Theoretical massNumber of molelcules
Total (without water)13,4441
Polymers13,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Prophage pi2 protein 01, integrase


Theoretical massNumber of molelcules
Total (without water)13,4441
Polymers13,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Prophage pi2 protein 01, integrase


Theoretical massNumber of molelcules
Total (without water)13,4441
Polymers13,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Prophage pi2 protein 01, integrase


Theoretical massNumber of molelcules
Total (without water)13,4441
Polymers13,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Prophage pi2 protein 01, integrase


Theoretical massNumber of molelcules
Total (without water)13,4441
Polymers13,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.704, 90.272, 156.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsStatic light scattering suggests that this domain is monomer in solution. Whereas in the crystal structure it forms a hexameric ring.

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Components

#1: Protein
Prophage pi2 protein 01, integrase


Mass: 13443.736 Da / Num. of mol.: 6 / Fragment: sequence database residues 54-156 / Mutation: P137C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: IL1403 / Gene: int, L364, L36404, LL1008, pi201 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9CGT4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 291 K / Method: microbatch, under oil / pH: 6.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Cacodylate acid (pH 6.5) and 20% PEG8k, Microbatch, under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 18, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 44148 / Num. obs: 34171 / % possible obs: 77.4 % / Observed criterion σ(F): 0.3 / Observed criterion σ(I): 0.3 / Redundancy: 4 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.059 / Net I/σ(I): 16.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.138 / % possible all: 56.6

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXfollowed by SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 220812.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1589 4.9 %RANDOM
Rwork0.26 ---
obs0.26 32489 73.2 %-
all-44383 --
Solvent computationSolvent model: FLAT MODEL / Bsol: -2.18399 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1-35.22 Å20 Å20 Å2
2---13.3 Å20 Å2
3----21.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.83 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 0 51 5239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 71 4.2 %
Rwork0.348 1621 -
obs--37.6 %

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