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- PDB-1z19: Crystal structure of a lambda integrase(75-356) dimer bound to a ... -

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Basic information

Entry
Database: PDB / ID: 1z19
TitleCrystal structure of a lambda integrase(75-356) dimer bound to a COC' core site
Components
  • 33-MER
  • 5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
  • 5'-D(P*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*TP*TP*A)-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 / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. ...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 / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / 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 / SAD / Resolution: 2.8 Å
AuthorsBiswas, T. / Aihara, H. / Radman-Livaja, M. / Filman, D. / Landy, A. / Ellenberger, T.
CitationJournal: Nature / Year: 2005
Title: A structural basis for allosteric control of DNA recombination by lambda integrase.
Authors: Biswas, T. / Aihara, H. / Radman-Livaja, M. / Filman, D. / Landy, A. / Ellenberger, T.
History
DepositionMar 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Remark 999SEQUENCE TRANSLATIONAL INITIATION

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(P*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*TP*TP*A)-3'
E: 33-MER
A: Integrase
B: Integrase


Theoretical massNumber of molelcules
Total (without water)85,7425
Polymers85,7425
Non-polymers00
Water55831
1
C: 5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(P*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*TP*TP*A)-3'
E: 33-MER
A: Integrase
B: Integrase

C: 5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(P*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*TP*TP*A)-3'
E: 33-MER
A: Integrase
B: Integrase


Theoretical massNumber of molelcules
Total (without water)171,48510
Polymers171,48510
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Unit cell
Length a, b, c (Å)109.297, 121.481, 65.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -X, -Y, Z

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Components

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


Mass: 4821.123 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*TP*TP*A)-3'


Mass: 6138.000 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 33-MER


Mass: 10203.638 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein Integrase /


Mass: 32289.775 Da / Num. of mol.: 2 / Fragment: core-binding and catatlytic domains / Mutation: E174K
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) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P03700
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG4000, Sodium citrate, DTT, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2Sodium citrate11
3DTT11
4H2O11
5PEG400012
6Sodium citrate12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 22116 / Num. obs: 21818 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.6

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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: SAD / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 2226 random
Rwork0.218 --
all0.218 22116 -
obs0.218 21818 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 1316 0 31 5677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3

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