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- PDB-1p7d: Crystal structure of the Lambda Integrase (residues 75-356) bound... -

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Basic information

Entry
Database: PDB / ID: 1p7d
TitleCrystal structure of the Lambda Integrase (residues 75-356) bound to DNA
Components
  • 26-MER
  • 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'
  • Integrase
KeywordsDNA Binding Protein/DNA / PROTEIN-DNA COMPLEX / DNA Binding Protein-DNA COMPLEX
Function / homology
Function and homology information


provirus excision / integrase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity ...provirus excision / integrase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity / symbiont entry into host cell / DNA binding
Similarity search - Function
Integrase, lambda-type, N-terminal DNA-binding / Bacteriophage lambda integrase, Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / : / Integrase, SAM-like, N-terminal / Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Phage integrase family / Core-binding (CB) domain ...Integrase, lambda-type, N-terminal DNA-binding / Bacteriophage lambda integrase, Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / : / Integrase, SAM-like, N-terminal / Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / 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-binding domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Integrase
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.95 Å
AuthorsAihara, H. / Kwon, H.J. / Nunes-Duby, S.E. / Landy, A. / Ellenberger, T.
CitationJournal: Mol.Cell / Year: 2003
Title: A Conformational Switch Controls the DNA Cleavage Activity of Lambda Integrase
Authors: Aihara, H. / Kwon, H.J. / Nunes-Duby, S.E. / Landy, A. / Ellenberger, T.
History
DepositionMay 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999translational initiation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'
D: 26-MER
E: 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'
F: 26-MER
A: Integrase
B: Integrase


Theoretical massNumber of molelcules
Total (without water)87,8016
Polymers87,8016
Non-polymers00
Water00
1
C: 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'
D: 26-MER
A: Integrase


Theoretical massNumber of molelcules
Total (without water)43,9003
Polymers43,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'
F: 26-MER
B: Integrase


Theoretical massNumber of molelcules
Total (without water)43,9003
Polymers43,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.021, 106.161, 73.165
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'


Mass: 3910.573 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 26-MER


Mass: 8075.239 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein Integrase


Mass: 31914.553 Da / Num. of mol.: 2 / Fragment: Residues 75-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: INT / Production host: Escherichia coli (E. coli) / References: UniProt: P03700
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: 2.78 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Ammonium Sulfate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Ammonium Sulfate11
3Sodium Cacodylate11
4H2O11
5PEG 800012
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium cacodylate1droppH6.5
218-30 %PEG80001drop
320-100 mMammonium sulfate1drop
430 %PEG80001reservoir
51

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 6, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 19010 / Num. obs: 19010 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.8
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1884 / % possible all: 99.9
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.95→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 929 4.9 %RANDOM
Rwork0.231 ---
all-19010 --
obs-19010 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 1600 0 0 5884
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it1.1871.5
X-RAY DIFFRACTIONc_scbond_it1.9912
X-RAY DIFFRACTIONc_mcangle_it2.0872
X-RAY DIFFRACTIONc_scangle_it3.3042.5
LS refinement shellResolution: 2.95→3.01 Å
RfactorNum. reflection% reflection
Rfree0.428 56 -
Rwork0.4 --
obs--99.9 %
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.401

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