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- PDB-3jtz: Structure of the arm-type binding domain of HPI integrase -

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Basic information

Entry
Database: PDB / ID: 3jtz
TitleStructure of the arm-type binding domain of HPI integrase
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / four stranded beta-sheet
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell / DNA binding
Similarity search - Function
Integrase, DNA-binding domain / Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / : / Phage integrase central domain / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. ...Integrase, DNA-binding domain / Integrase, DNA-binding domain / Integrase, DNA-binding domain superfamily / Arm DNA-binding domain / : / Phage integrase central domain / : / 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 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSzwagierczak, A. / Antonenka, U. / Popowicz, G.M. / Sitar, T. / Holak, T.A. / Rakin, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structures of the arm-type binding domains of HPI and HAI7 integrases
Authors: Szwagierczak, A. / Antonenka, U. / Popowicz, G.M. / Sitar, T. / Holak, T.A. / Rakin, A.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_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

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1262
Polymers10,1031
Non-polymers231
Water2,252125
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2514
Polymers20,2052
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1480 Å2
ΔGint-35 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.750, 48.750, 74.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-74-

MET

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Components

#1: Protein Integrase / CP4-like integrase / Int protein / Putative prophage integrase


Mass: 10102.696 Da / Num. of mol.: 1 / Fragment: Arm-type binding domain, UNP residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: int, int2 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z3B4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M tri-sodium citrate, pH5.6, 35% tert-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 26, 2009 / Details: mirror
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9873 Å / Relative weight: 1
ReflectionResolution: 1.3→10 Å / Num. all: 22769 / Num. obs: 19463 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 29.07
Reflection shellResolution: 1.3→1.4 Å / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 8.98 / % possible all: 65.5

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0066refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→10 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 0.854 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.064 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23867 963 5 %RANDOM
Rwork0.2125 ---
obs0.2138 18404 85.35 %-
all-22769 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms604 0 1 125 730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022617
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.281.993828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.692576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38921.30423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59615118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.942156
X-RAY DIFFRACTIONr_chiral_restr0.0790.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021447
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8051.5382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5462610
X-RAY DIFFRACTIONr_scbond_it2.1513235
X-RAY DIFFRACTIONr_scangle_it3.4424.5218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 40 -
Rwork0.226 786 -
obs--50.83 %

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