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- PDB-1cxu: 1.42A RESOLUTION ASV INTEGRASE CORE DOMAIN FROM CITRATE -

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Basic information

Entry
Database: PDB / ID: 1cxu
Title1.42A RESOLUTION ASV INTEGRASE CORE DOMAIN FROM CITRATE
ComponentsPROTEIN (AVIAN SARCOMA VIRUS INTEGRASE)
KeywordsTRANSFERASE / MIXED BETA-SHEET SURROUNDED BY ALPHA-HELICES
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesAvian sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å
AuthorsLubkowski, J. / Dauter, Z. / Yang, F. / Alexandratos, J. / Wlodawer, A.
Citation
Journal: Biochemistry / Year: 1999
Title: Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant.
Authors: Lubkowski, J. / Dauter, Z. / Yang, F. / Alexandratos, J. / Merkel, G. / Skalka, A.M. / Wlodawer, A.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: High Resolution Structure of the Catalytic Domain of Avian Sarcoma Virus Integrase
Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M.
History
DepositionAug 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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_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: PROTEIN (AVIAN SARCOMA VIRUS INTEGRASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1403
Polymers17,8551
Non-polymers2842
Water3,657203
1
A: PROTEIN (AVIAN SARCOMA VIRUS INTEGRASE)
hetero molecules

A: PROTEIN (AVIAN SARCOMA VIRUS INTEGRASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2796
Polymers35,7112
Non-polymers5684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)66.177, 66.177, 78.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (AVIAN SARCOMA VIRUS INTEGRASE)


Mass: 17855.441 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN / Mutation: INS(P48, L49, R50, E51, N208, L209)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian sarcoma virus / Genus: Alpharetrovirus / Strain: ROUS SARCOMA VIRUS, SCHMIDT-RUPPIN B / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, UniProt: O92956*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A ...THE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A RESULT OF VIRAL STRAIN VARIATION. THE STRAIN USED FOR THIS WORK, "ROUS SARCOMA VIRUS SCHMIDT-RUPPIN B", COMPARED TO "POL-RSVP" SEQUENCE DIFFERS AT TWO POSITIONS WITH THE CONSERVATIVE AMINO ACID RESIDUE DIFFERENCES NOTED (VAL->ALA 101 & ARG->LYS 166).

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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 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5 / Details: Bujacz, G., (1995) J. Mol. Biol., 253, 333.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
210 %isopropanol1reservoir
36-7.5 mg/mlprotein1drop
420 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.42→13 Å / Num. all: 34367 / Num. obs: 34287 / % possible obs: 99 % / Observed criterion σ(F): -3 / Redundancy: 5.55 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.7
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 357298
Reflection shell
*PLUS
% possible obs: 98.9 % / Mean I/σ(I) obs: 5.2

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.42→10 Å / Num. parameters: 536 / Num. restraintsaints: 467 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1142 -RANDOM
Rwork0.187 ---
all0.187 34287 --
obs0.187 34287 99.1 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1308
Refinement stepCycle: LAST / Resolution: 1.42→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 19 203 1323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 0 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_plane_restr0.025

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