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- PDB-1ae9: STRUCTURE OF THE LAMBDA INTEGRASE CATALYTIC CORE -

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Basic information

Entry
Database: PDB / ID: 1ae9
TitleSTRUCTURE OF THE LAMBDA INTEGRASE CATALYTIC CORE
ComponentsLAMBDA INTEGRASE
KeywordsDNA RECOMBINATION / INTEGRASE / SITE-SPECIFIC RECOMBINATION
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 / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsKwon, H.J. / Tirumalai, R. / Landy, A. / Ellenberger, T.
CitationJournal: Science / Year: 1997
Title: Flexibility in DNA recombination: structure of the lambda integrase catalytic core.
Authors: Kwon, H.J. / Tirumalai, R. / Landy, A. / Ellenberger, T.
History
DepositionMar 6, 1997Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAMBDA INTEGRASE
B: LAMBDA INTEGRASE


Theoretical massNumber of molelcules
Total (without water)40,5262
Polymers40,5262
Non-polymers00
Water3,513195
1
A: LAMBDA INTEGRASE
B: LAMBDA INTEGRASE

A: LAMBDA INTEGRASE
B: LAMBDA INTEGRASE

A: LAMBDA INTEGRASE
B: LAMBDA INTEGRASE


Theoretical massNumber of molelcules
Total (without water)121,5796
Polymers121,5796
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)107.320, 107.320, 108.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.760913, -0.648655, 0.016068), (-0.648564, 0.76108, 0.011035), (-0.019387, -0.002025, -0.99981)
Vector: 60.67719, 10.98542, 46.91213)

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Components

#1: Protein LAMBDA INTEGRASE


Mass: 20263.154 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN / Mutation: Y342F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Production host: Escherichia coli (E. coli) / References: UniProt: P03700
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.15
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 8000 75 MM NACL 7 MM MGCL2 50 MM MES, PH 6.15 40 MM NACITRATE 1 MM DTT 1 MM SPERMINE
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
126 mg/mlc1701drop
250 mMMES1reservoir
375 mM1reservoirNaCl
47 mM1reservoirMgCl2
540 mMsodium citrate1reservoir
61 mMDTT1reservoir
70.1 mMEDTA1reservoir
81 mMspermine-HCl1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→16 Å / Num. obs: 110468 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.042 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4 / Rsym value: 0.251 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 36385 / Num. measured all: 110468 / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→16 Å / Rfactor Rfree error: 0.0038 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3686 10 %RANDOM
Rwork0.199 ---
obs0.199 36385 98.9 %-
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-4.03 Å21.91 Å20 Å2
2--4.03 Å20 Å2
3----6.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 0 195 2819
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.178
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.131
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.0971.5
X-RAY DIFFRACTIONx_mcangle_it2.2532
X-RAY DIFFRACTIONx_scbond_it1.8082
X-RAY DIFFRACTIONx_scangle_it3.5042.5
LS refinement shellResolution: 1.9→1.93 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 189 10 %
Rwork0.309 1642 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.ALL
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.131
LS refinement shell
*PLUS
Rfactor Rfree: 0.32

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