1czb

ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM HEPES

Method: X-RAY DIFFRACTION D_max: 53.7 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

AVIAN SARCOMA VIRUS INTEGRASE

Avian sarcoma virus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 624–779	Fragment：CATALYTIC CORE DOMAIN Mutation：INS(P48, L49, R50, E51, N208, L209)	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% PEG 4000, 10% ISOPROPANOL, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.06 Å R-free 0.164

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1CZB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A5V ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 AND MN CATION Deposited 1998-02-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN	Not recorded	MN MANGANESE (II) ION × 2 Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA HEPES, PH 7.5	Resolution 1.90 Å R-free 0.210
1A5V ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 AND MN CATION Deposited 1998-02-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN	Not recorded	MN MANGANESE (II) ION × 2 Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA HEPES, PH 7.5	Resolution 1.90 Å R-free 0.210
1A5W ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 Deposited 1998-02-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN	Not recorded	Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.6	Resolution 2.00 Å R-free 0.222
1A5X ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 Deposited 1998-02-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN	Not recorded	Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% PEG 4000, 10% ISOPROPANOL, 0.1M HEPES, PH 7.5	Resolution 1.90 Å R-free 0.212
1ASU AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 2% PEG 400, 2M AMMONIUM SULFATE, HEPES PH 7.5 Deposited 1995-08-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa）	Mutation：INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209)	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.70 Å R-free 0.188
1ASV Avian sarcoma virus integrase catalytic core domain Deposited 1995-08-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa）	Mutation：INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.20 Å R-free 0.234
1ASW AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, HEPES PH 7.5 USING SELENOMETHIONINE SUBSTITUTED PROTEIN; DATA COLLECTED AT-165 DEGREES C Deposited 1995-08-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa）	Mutation：INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209) Non-standard monomer：Yes (specific site not provided by mmCIF)	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.208
1C0M CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE Deposited 1999-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 621–858（238 aa） Fragment：RESIDUES 49-286 Chain B 621–858（238 aa） Fragment：RESIDUES 49-286	Mutation：F199K Mutation：F199K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION METHOD；pH 7；277 K；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	Resolution 2.53 Å R-free 0.279
1C0M CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE Deposited 1999-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 621–858（238 aa） Fragment：RESIDUES 49-286 Chain D 621–858（238 aa） Fragment：RESIDUES 49-286	Mutation：F199K Mutation：F199K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION METHOD；pH 7；277 K；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	Resolution 2.53 Å R-free 0.279
1C1A CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE Deposited 1999-07-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 621–858（238 aa） Fragment：RESIDUES 49-286 Chain B 621–858（238 aa） Fragment：RESIDUES 49-286	Mutation：F199K Mutation：F199K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions ROD-SHAPED CRYSTALS WERE GROWN BY SITTING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.1M SODIUM CACODYLATE, 0.02M IMIDAZOLE, PH 7.2, 10% PEG3350, AND 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML)	Resolution 3.10 Å R-free 0.337
1CXQ ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM AMMONIUM SULFATE Deposited 1999-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN	Mutation：INS(P48, L49, R50, E51, N208, L209)	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2% Peg 400, 2M Ammonium Sulfate, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.02 Å R-free 0.157
1CXU 1.42A RESOLUTION ASV INTEGRASE CORE DOMAIN FROM CITRATE Deposited 1999-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN	Mutation：INS(P48, L49, R50, E51, N208, L209)	CIT CITRIC ACID × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；20% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.42 Å R-free 0.221
1CZ9 ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN (D64N) FROM CITRATE Deposited 1999-09-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN	Mutation：D64N, INS(P48, L49, R50, E51, N208, L209)	SO4 SULFATE ION × 2 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；20% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.20 Å R-free 0.150
1VSD ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, HIGH MG CONCENTRATION FORM Deposited 1995-11-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 616–771（156 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLI-MOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 500 MILLI-MOLAR MGCL2.	Resolution 1.70 Å R-free 0.191
1VSE ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM Deposited 1995-11-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLIMOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 20 MILLIMOLAR MGCL2.	Resolution 2.20 Å R-free 0.201
1VSF ASV INTEGRASE CORE DOMAIN WITH MN(II) COFACTOR AND HEPES LIGAND, HIGH MG CONCENTRATION FORM Deposited 1995-11-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209	Not recorded	MN MANGANESE (II) ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLIMOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 10 MILLIMOLAR MNCL2.	Resolution 2.05 Å R-free 0.189
1VSH ASV INTEGRASE CORE DOMAIN WITH ZN(II) COFACTORS Deposited 1997-03-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM ZNCL2.	Resolution 1.95 Å
1VSI ASV INTEGRASE CORE DOMAIN WITH CA(II) COFACTOR Deposited 1997-03-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM CACL2.	Resolution 2.20 Å
1VSJ ASV INTEGRASE CORE DOMAIN WITH CD(II) COFACTORS Deposited 1997-03-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209	Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, N10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM CDCL2.	Resolution 2.10 Å
1VSK ASV INTEGRASE CORE DOMAIN D64N MUTATION IN CITRATE BUFFER PH 6.0 Deposited 1998-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN	Mutation：D64N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.6	Resolution 2.20 Å R-free 0.249
1VSL ASV INTEGRASE CORE DOMAIN D64N MUTATION WITH ZINC CATION Deposited 1998-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN	Mutation：D64N	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.6	Resolution 2.20 Å R-free 0.244
1VSM ASV INTEGRASE CORE DOMAIN IN CITRATE BUFFER PH 5.0 Deposited 1998-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.0, pH 5.6	Resolution 2.15 Å R-free 0.238
3TIR Pseudo-atomic model of the Rous Sarcoma Virus capsid hexamer Deposited 2011-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 240–465（226 aa） Fragment：UNP resides 240-465	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.3；291.15 K；2-7 %(w/v) PEG 8000 0.2M CAPS/KOH, pH 10.3, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 4.10 Å R-free 0.391
4FW1 Crystal structure of two-domain RSV INTEGRASE covalently linked with DNA Deposited 2012-06-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1329–1550（222 aa） Fragment：UNP residues 1329-1580 Chain B 1329–1550（222 aa） Fragment：UNP residues 1329-1580	Mutation：S124D, C125A, E157C, R166K, F199K Mutation：S124D, C125A, E157C, R166K, F199K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5% Ethanol, 10% PEG4,000, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.86 Å R-free 0.222
4FW2 Crystal structure of RSV three-domain integrase with disordered N-terminal domain Deposited 2012-06-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1281–1550（270 aa） Fragment：UNP residues 1281-1550 Chain B 1281–1550（270 aa） Fragment：UNP residues 1281-1550	Mutation：C23S, R166K, F199K Mutation：C23S, R166K, F199K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% ethanol, 100 mM imidazole-HCl, and 5% PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.65 Å R-free 0.244
5EJK Crystal structure of the Rous sarcoma virus intasome Deposited 2015-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: hexadecameric	Chain A 1281–1550（270 aa） Fragment：UNP residues 573-842 Chain B 1281–1550（270 aa） Fragment：UNP residues 573-842 Chain C 1281–1550（270 aa） Fragment：UNP residues 573-842 Chain D 1281–1550（270 aa） Fragment：UNP residues 573-842 Chain E 1281–1550（270 aa） Fragment：UNP residues 573-842 Chain F 1281–1550（270 aa） Fragment：UNP residues 573-842 Chain G 1281–1550（270 aa） Fragment：UNP residues 573-842 Chain H 1281–1550（270 aa） Fragment：UNP residues 573-842	Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 W TUNGSTEN ION × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；Sodium formate	Resolution 3.80 Å R-free 0.294
5KZ9 Crystal structure of the Rous sarcoma virus matrix protein. Deposited 2016-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：UNP residues 1-155	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.3；293 K；2.60 M Ammonium formate, 0.20 M Beta-Alanine/KOH pH 10.3	Resolution 2.85 Å R-free 0.239
5KZ9 Crystal structure of the Rous sarcoma virus matrix protein. Deposited 2016-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–155（155 aa） Fragment：UNP residues 1-155	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.3；293 K；2.60 M Ammonium formate, 0.20 M Beta-Alanine/KOH pH 10.3	Resolution 2.85 Å R-free 0.239
5KZA Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I41 Deposited 2016-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–102（101 aa） Fragment：UNP residues 2-102	Not recorded	NO3 NITRATE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；18%(w/v) PEG 8000, 0.2 M Succinic acid/KOH pH 5.5, 1.0 M Ammonium nitrate	Resolution 1.86 Å R-free 0.210
5KZA Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I41 Deposited 2016-07-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–102（101 aa） Fragment：UNP residues 2-102	Not recorded	NO3 NITRATE ION × 4 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；18%(w/v) PEG 8000, 0.2 M Succinic acid/KOH pH 5.5, 1.0 M Ammonium nitrate	Resolution 1.86 Å R-free 0.210
5KZB Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I4122 Deposited 2016-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–102（101 aa） Fragment：UNP residues 2-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；291.15 K；0.6 M Malonic acid /KOH pH 9.1, 0.1 M Boric acid /KOH pH 9.1	Resolution 3.20 Å R-free 0.249
5KZB Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I4122 Deposited 2016-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–102（101 aa） Fragment：UNP residues 2-102	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；291.15 K；0.6 M Malonic acid /KOH pH 9.1, 0.1 M Boric acid /KOH pH 9.1	Resolution 3.20 Å R-free 0.249
6CCJ NMR structure of the Rous sarcoma virus matrix protein (M domain) Deposited 2018-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–87（86 aa）	Mutation：M1S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1 NMR sample composition 0.5 mM [U-95% 13C; U-95% 15N] RSV MA, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition .5 mM [U-95% 15N] Matrix protein, 50 mM sodium phosphate, 50 mM sodium chloride, 2 M TCEP, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-95% 13C] Matrix protein, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM TCEP, 100% D2O \| 100% D2O	Resolution not provided
6CE5 NMR structure of the Rous sarcoma virus matrix protein (M-domain) in the presence of myo-inositol hexakisphosphate Deposited 2018-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa）	Mutation：M1S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1 NMR sample composition 0.5 mM [U-95% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM tcep, 2 mM IP6, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-95% 13C; U-95% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM tcep, 2 mM IP6, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6CUS HADDOCK structure of the Rous sarcoma virus matrix protein (M-domain) in complex with myo-inositol hexakisphosphate Deposited 2018-03-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa）	Mutation：M1S	IHP INOSITOL HEXAKISPHOSPHATE × 1	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 500 uM [U-98% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 2 mM INOSITOL HEXAKISPHOSPHATE, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-98% 13C] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 2 mM INOSITOL HEXAKISPHOSPHATE, 100% D2O \| 100% D2O	Resolution not provided
6CV8 HADDOCK structure of the Rous sarcoma virus matrix protein (M-domain) in complex with inositol 1,4,5-trisphosphate Deposited 2018-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa）	Mutation：M1S	I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 100 uM [U-98% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 1.6 mM D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6CW4 HADDOCK structure of the Rous sarcoma virus matrix protein (M-domain) in complex with inositol 1,3,5-trisphosphate Deposited 2018-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–87（87 aa） Fragment：residues 1-87	Mutation：M1S	FGV (1R,2S,3r,4R,5S,6s)-2,4,6-trihydroxycyclohexane-1,3,5-triyl tris[dihydrogen (phosphate)] × 1	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 100 uM [U-98% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 1.6 mM IP3, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7JN3 Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048 Deposited 2020-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain B 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain C 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain D 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain E 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain F 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain G 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain H 1281–1558（278 aa） Fragment：UNP residues 1281-1558	Not recorded	ZN ZINC ION × 2 ZZX (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
7KU7 Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. Cluster identified by 3-dimensional variability analysis in cryoSPARC. Deposited 2020-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1281–1558（278 aa） Chain B 1281–1558（278 aa） Chain C 1281–1558（278 aa） Chain D 1281–1558（278 aa） Chain E 1281–1558（278 aa） Chain F 1281–1558（278 aa） Chain G 1281–1558（278 aa） Chain H 1281–1558（278 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 4 ZZX (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7KUI Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. CIC region of a cluster identified by 3-dimensional variability analysis in cryoSPARC. Deposited 2020-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 1281–1558（278 aa） Chain B 1281–1558（278 aa） Chain C 1281–1558（278 aa） Chain D 1281–1558（278 aa） Chain E 1281–1558（278 aa） Chain F 1281–1558（278 aa） Chain G 1281–1558（278 aa） Chain H 1281–1558（278 aa）	Not recorded	ZN ZINC ION × 2 ZZX (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8E14 Cryo-EM structure of Rous sarcoma virus strand transfer complex Deposited 2022-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: tetradecameric	Chain A 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain B 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain C 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain D 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain E 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain F 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain G 1281–1558（278 aa） Fragment：UNP residues 1281-1558 Chain H 1281–1558（278 aa） Fragment：UNP residues 1281-1558	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å

36 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_RSVP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–160； UniProt 624–779

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1czb
Deposition date deposition_date	1999-09-01
Structure title title	ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM HEPES
Keywords keywords	MIXED BETA-SHEET SURROUNDED BY ALPHA-HELICES, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.25 Å
Radius of gyration Rg (electron density) rg_electron	15.23 Å
Forward intensity I(0) i0	4906570.00
Molecular weight molecular_weight	15676.0 kDa
Excluded volume excluded_volume	19598 Å³
Envelope volume envelope_volume	22401 Å³
Hydration-shell volume shell_volume	12736 Å³
Envelope diameter envelope_diameter	56.0 Å
Shell Rg shell_rg	20.70 Å
Envelope Rg envelope_rg	15.70 Å
Shape Rg shape_rg	15.18 Å
Total Rg total_rg	16.40 Å
Total atoms total_atoms	1101
Residues n_residues	141
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	53.7 Å
Rg (real space) rg_real	16.22 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	4.9070e+06
I(0) uncertainty (real space) i0_real_error	5.4490e+04
Rg (reciprocal space) rg_reciprocal	16.22 Å
I(0) (reciprocal space) i0_reciprocal	4907000.0000
Solution quality estimate total_estimate	0.6542
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.5 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.265
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1025000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 0.353; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	AVIAN SARCOMA VIRUS INTEGRASE
Molecular weight formula_weight	17855.4 kDa
Mutation mutation	INS(P48, L49, R50, E51, N208, L209)
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1283

PLREGRGLGPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAAQHHWATAIAVLGRPKAIKTDNGSCFTSKSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTNL

来源 Source

来源生物 organism	Avian sarcoma virus
NCBI Class编号 ncbi_taxonomy_id	11876
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1czba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.2 — Retroviral integrase, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id	1czbA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

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8. Citations (1)

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Unit-cell length a length_a	65.370 Å
Unit-cell length b length_b	65.370 Å
Unit-cell length c length_c	80.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.060 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1430
R_work r_work	0.1433
R_free r_free	0.1639

fit	/app/data/saxs_computation/cz/1czb/1czb.fit
pddf	/app/data/pr_computation/cz/1czb/1czb.pr.out
profile	/app/data/saxs_computation/cz/1czb/1czb.dat