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- PDB-1z1b: Crystal structure of a lambda integrase dimer bound to a COC' cor... -

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Basic information

Entry
Database: PDB / ID: 1z1b
TitleCrystal structure of a lambda integrase dimer bound to a COC' core site
Components
  • (26-MER DNA) x 2
  • 29-MER DNA
  • 5'-D(*CP*T*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
  • 5'-D(*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*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 / Classic Zinc Finger / DNA-binding domain superfamily / Double Stranded RNA Binding Domain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Integrase
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.8 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
Revision 1.4Apr 13, 2022Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.5Oct 30, 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
C: 5'-D(*CP*T*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*T)-3'
E: 29-MER DNA
F: 26-MER DNA
G: 26-MER DNA
A: Integrase
B: Integrase


Theoretical massNumber of molelcules
Total (without water)115,5727
Polymers115,5727
Non-polymers00
Water00
1
C: 5'-D(*CP*T*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*T)-3'
E: 29-MER DNA
F: 26-MER DNA
G: 26-MER DNA
A: Integrase
B: Integrase

C: 5'-D(*CP*T*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*T)-3'
E: 29-MER DNA
F: 26-MER DNA
G: 26-MER DNA
A: Integrase
B: Integrase


Theoretical massNumber of molelcules
Total (without water)231,14414
Polymers231,14414
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)97.599, 211.278, 191.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: X-1, -Y, -Z

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Components

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DNA chain , 5 types, 5 molecules CDEFG

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


Mass: 4227.749 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*T)-3'


Mass: 5520.600 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 29-MER DNA


Mass: 8943.826 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 26-MER DNA


Mass: 7949.171 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain 26-MER DNA


Mass: 8024.173 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#6: Protein Integrase


Mass: 40453.215 Da / Num. of mol.: 2 / 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

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Details

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: 4.22 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG4000, Sodium citrate, isopropanol, DTT, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2Sodium citrate11
3isopropanol11
4DTT11
5H2O11
6PEG40012
7Sodium citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 13, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. all: 22756 / Num. obs: 22529 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.65→3.78 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
SHARPphasing
REFMAC5.1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.296 963 random
Rwork0.248 --
all0.248 20004 -
obs0.248 19646 -
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 2199 0 0 7653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.5

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