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- PDB-1c0m: CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE -

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Basic information

Entry
Database: PDB / ID: 1c0m
TitleCRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE
ComponentsPROTEIN (INTEGRASE)
KeywordsTRANSFERASE / INTEGRASE / ROUS SARCOMA VIRUS / HIV / PROTEIN STRUCTURE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / 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, C-terminal domain superfamily, retroviral / 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 / SH3 type barrels. / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsYang, Z.-N. / Mueser, T.C. / Bushman, F.D. / Hyde, C.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase.
Authors: Yang, Z.N. / Mueser, T.C. / Bushman, F.D. / Hyde, C.C.
History
DepositionJul 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (INTEGRASE)
B: PROTEIN (INTEGRASE)
C: PROTEIN (INTEGRASE)
D: PROTEIN (INTEGRASE)


Theoretical massNumber of molelcules
Total (without water)106,3984
Polymers106,3984
Non-polymers00
Water2,540141
1
A: PROTEIN (INTEGRASE)
B: PROTEIN (INTEGRASE)


Theoretical massNumber of molelcules
Total (without water)53,1992
Polymers53,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-26 kcal/mol
Surface area20560 Å2
MethodPISA
2
C: PROTEIN (INTEGRASE)
D: PROTEIN (INTEGRASE)


Theoretical massNumber of molelcules
Total (without water)53,1992
Polymers53,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-28 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.752, 66.369, 76.670
Angle α, β, γ (deg.)67.47, 78.61, 90.18
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
PROTEIN (INTEGRASE) / E.C.2.7.7.49


Mass: 26599.531 Da / Num. of mol.: 4 / Fragment: RESIDUES 49-286 / Mutation: F199K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, RNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.4 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion method / pH: 7
Details: PLATE-SHAPED CRYSTALS WERE INFREQUENTLY GROWN BY HANGING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.05M SODIUM CACODYLATE, PH 7.0, 10% PEG 3350, and ...Details: PLATE-SHAPED CRYSTALS WERE INFREQUENTLY GROWN BY HANGING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.05M SODIUM CACODYLATE, PH 7.0, 10% PEG 3350, and 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML), HANGING DROP VAPOR DIFFUSION METHOD, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 M1reservoirKCl
20.01 M1reservoirMgCl2
30.05 Msodium cacodylate1reservoir
410 %(w/v)PEG33501reservoir
525 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9672
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9672 Å / Relative weight: 1
ReflectionResolution: 2.53→15 Å / Num. obs: 28842 / % possible obs: 87.6 % / Observed criterion σ(I): 0.04 / Redundancy: 1.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.3
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 5.4 / % possible all: 75.7
Reflection shell
*PLUS
% possible obs: 75.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
CNSrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A POLYALANINE 1C1A INITIAL MODEL BUILT FROM 3.2A MAD PHASED MAP, WITHOUT RESIDUES 200-220

1c1a


Resolution: 2.53→15 Å / Cross valid method: THROUGHOUT / σ(F): 0.2
Details: CAUTION SHOULD BE TAKEN IN INTERPRETING THOSE RESIDUES WITH B FACTORS IN UPPER 50S OR HIGHER
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1443 5 %RANDOM
Rwork0.216 ---
obs0.216 27399 87.6 %-
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.355 Å2-2.813 Å23.866 Å2
2---0.276 Å25.223 Å2
3----1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.53→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6893 0 0 141 7034
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.82
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.675
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.669
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight Biso Weight position
11GROUP 1: CHAIN A AND CX-RAY DIFFRACTION0.052150
22GROUP 2: CHAIN B AND DX-RAY DIFFRACTION0.062150
LS refinement shellResolution: 2.53→2.62 Å
RfactorNum. reflection% reflection
Rfree0.347 140 4.3 %
Rwork0.286 2332 -
obs--75.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: 'CNS, X-PLOR 3.851' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.82

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