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- PDB-1aih: CATALYTIC DOMAIN OF BACTERIOPHAGE HP1 INTEGRASE -

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Basic information

Entry
Database: PDB / ID: 1aih
TitleCATALYTIC DOMAIN OF BACTERIOPHAGE HP1 INTEGRASE
ComponentsHP1 INTEGRASE
KeywordsDNA INTEGRATION / RECOMBINATION
Function / homology
Function and homology information


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
Phage integrase, N-terminal domain / : / Intergrase catalytic core / 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 ...Phage integrase, N-terminal domain / : / Intergrase catalytic core / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHaemophilus phage HP1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHickman, A.B. / Waninger, S. / Scocca, J.J. / Dyda, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Molecular organization in site-specific recombination: the catalytic domain of bacteriophage HP1 integrase at 2.7 A resolution.
Authors: Hickman, A.B. / Waninger, S. / Scocca, J.J. / Dyda, F.
History
DepositionApr 17, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HP1 INTEGRASE
B: HP1 INTEGRASE
C: HP1 INTEGRASE
D: HP1 INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,71917
Polymers77,8294
Non-polymers89013
Water2,738152
1
A: HP1 INTEGRASE
B: HP1 INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4449
Polymers38,9152
Non-polymers5297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-126 kcal/mol
Surface area16260 Å2
MethodPISA
2
C: HP1 INTEGRASE
D: HP1 INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2768
Polymers38,9152
Non-polymers3616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-99 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.400, 129.300, 234.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9998, -0.0133, -0.0154), (-0.0082, -0.4296, 0.903), (-0.0187, 0.9029, 0.4294)1.4576, 67.1685, -42.4
2given(-0.8897, -0.4564, 0.0112), (-0.452, 0.884, 0.1193), (-0.0644, 0.1011, -0.9928)16.0796, -9.585, 222.5898

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Components

#1: Protein
HP1 INTEGRASE


Mass: 19457.312 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 168 - 337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus phage HP1 (virus) / Genus: P2-like viruses / Strain: HP1C1 / Cell line: HAEMOPHILUS INFLUENZAE L10 / Gene: GENBANK U24159 / Plasmid: PHPC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P21442
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: VAPOR DIFFUSION, 15% PEG 8000, 45MM NA CAODYLATE, 34MM AMMONIUM SULFATE, 10MM TRIS-HCL, 4.5% GLYCEROL, 0.1 M MGCL., pH 7.5, vapor diffusion
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
215-17 %PEG80001reservoir
30.2 Mmagnesium acetate1reservoir
40.1 Msodium cacodylate1reservoir
5ammonium sulfate1drop

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.6498
DetectorType: PRINCETON 2K / Detector: CCD / Date: Dec 12, 1996 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6498 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 34819 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 11.4
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5 / Rsym value: 0.18 / % possible all: 89.7
Reflection
*PLUS
Num. measured all: 52126
Reflection shell
*PLUS
% possible obs: 89.7 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1849 5 %RANDOM
Rwork0.209 ---
obs0.209 36851 97.47 %-
Displacement parametersBiso mean: 47.77 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 45 156 5564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.31
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.48
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.225
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.369 110 4.2 %
Rwork0.318 2230 -
obs--82.98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19_MOD.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.48
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.225
LS refinement shell
*PLUS
Rfactor obs: 0.318

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