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- PDB-8wf7: The Crystal Structure of integrase from Biortus -

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Basic information

Entry
Database: PDB / ID: 8wf7
TitleThe Crystal Structure of integrase from Biortus
ComponentsIntegrase
KeywordsTRANSFERASE / Endonuclease / DNA integration / Metal-binding
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core ...Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ACETATE ION / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of integrase from Biortus
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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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)17,8408
Polymers17,2051
Non-polymers6357
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-14 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.027, 71.027, 66.849
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

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Components

#1: Protein Integrase /


Mass: 17204.553 Da / Num. of mol.: 1 / Mutation: C56S,F139D,F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: F2WR39
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM sodium acetate at pH 5.3, 1.9M ammonium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953743 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953743 Å / Relative weight: 1
ReflectionResolution: 1.55→45.306 Å / Num. obs: 28716 / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.1
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2019 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→45.306 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.062 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1986 1449 5.046 %
Rwork0.1761 27267 -
all0.177 --
obs-28716 99.979 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.086 Å20.043 Å20 Å2
2--0.086 Å2-0 Å2
3----0.278 Å2
Refinement stepCycle: LAST / Resolution: 1.55→45.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 34 137 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121273
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161178
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.6431737
X-RAY DIFFRACTIONr_angle_other_deg0.4191.5722756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.1554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42610225
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6721053
X-RAY DIFFRACTIONr_chiral_restr0.0570.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
X-RAY DIFFRACTIONr_nbd_refined0.2350.2249
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.21006
X-RAY DIFFRACTIONr_nbtor_refined0.180.2605
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.229
X-RAY DIFFRACTIONr_nbd_other0.2090.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.229
X-RAY DIFFRACTIONr_mcbond_it1.9072.531621
X-RAY DIFFRACTIONr_mcbond_other1.9082.529620
X-RAY DIFFRACTIONr_mcangle_it3.0573.77775
X-RAY DIFFRACTIONr_mcangle_other3.0553.779776
X-RAY DIFFRACTIONr_scbond_it2.7662.968652
X-RAY DIFFRACTIONr_scbond_other2.7642.969653
X-RAY DIFFRACTIONr_scangle_it4.3294.298955
X-RAY DIFFRACTIONr_scangle_other4.3264.3956
X-RAY DIFFRACTIONr_lrange_it6.61143.3191499
X-RAY DIFFRACTIONr_lrange_other6.39538.6571455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.55-1.590.272850.25120190.25121060.960.9799.9050.251
1.59-1.6340.2181160.21619330.21620490.9710.9761000.216
1.634-1.6810.1841120.20618570.20519690.9820.9771000.206
1.681-1.7330.261970.19718380.19919350.9630.9771000.197
1.733-1.790.227880.18417630.18618510.9670.981000.184
1.79-1.8520.197990.17317230.17418220.9760.9811000.173
1.852-1.9220.191030.17316750.17417780.9780.9821000.173
1.922-20.188800.16415810.16516610.9770.9841000.164
2-2.0890.197990.16515370.16616380.9760.98499.87790.165
2.089-2.1910.187920.16614470.16715390.980.9841000.166
2.191-2.3090.186780.1614170.16114950.980.9851000.16
2.309-2.4490.177710.16913390.1714100.9820.9831000.169
2.449-2.6170.192770.1512500.15213270.9810.9861000.15
2.617-2.8260.139560.15811590.15712150.9880.9841000.158
2.826-3.0950.159350.15911100.15911450.9880.9841000.159
3.095-3.4580.2330.17110090.17210420.9720.9821000.171
3.458-3.9890.208450.1558870.1589330.9750.98499.89280.155
3.989-4.8760.221430.1667520.1697950.970.9831000.166
4.876-6.8560.253340.255960.256300.9710.9661000.25
6.856-45.3060.23160.2393750.2393810.9770.9691000.239

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