10 20 30 40 50 60 70 80 3SSF - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA/DNA 08-JUL-11 3SSF
TITLE CRYSTAL STRUCTURE OF RNA:DNA DODECAMER CORRESPONDING TO HIV-1 TITLE 2 POLYPURINE TRACT, AT 1.6 A RESOLUTION.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*A)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS POLYPURINE TRACT (PPT) OF HIV-1; RNA-DNA HYBRID; REVERSE KEYWDS 2 TRANSCRIPTION, RNA-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR P.DROZDZAL,K.MICHALSKA,R.KIERZEK,L.LOMOZIK,M.JASKOLSKI
REVDAT 2 28-MAR-12 3SSF 1 JRNL REVDAT 1 08-FEB-12 3SSF 0
JRNL AUTH P.DROZDZAL,K.MICHALSKA,R.KIERZEK,L.LOMOZIK,M.JASKOLSKI JRNL TITL STRUCTURE OF AN RNA/DNA DODECAMER CORRESPONDING TO THE HIV-1 JRNL TITL 2 POLYPURINE TRACT AT 1.6 ANGSTROM RESOLUTION JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 169 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 22281746 JRNL DOI 10.1107/S0907444911053327
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.L.KOPKA,L.LAVELLE,G.W.HAN,H.-L.NG,R.E.DICKERSON REMARK 1 TITL AN UNUSUAL SUGAR CONFORMATION IN THE STRUCTURE OF AN RNA/DNA REMARK 1 TITL 2 DECAMER OF THE POLYPURINE TRACT MAY AFFECT RECOGNITION BY REMARK 1 TITL 3 RNASE H. REMARK 1 REF J.MOL.BIOL. V. 334 653 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.W.HAN,M.L.KOPKA,D.LANGS,M.R.SAWAYA,R.E.DICKERSON REMARK 1 TITL CRYSTAL STRUCTURE OF AN RNA.DNA HYBRID REVEALS REMARK 1 TITL 2 INTERMOLECULAR INTERCALATION: DIMER FORMATION BY BASE-PAIR REMARK 1 TITL 3 SWAPPING. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 100 9214 2003 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.G SARAFIANOS,K.DAS,C.TANTILLO,A.D.CLARK JR.,J.DING, REMARK 1 AUTH 2 J.M.WHITCOMB,P.L.BOYER,S.H.HUGHES,E.ARNOLD REMARK 1 TITL CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX REMARK 1 TITL 2 WITH A POLYPURINE TRACT RNA:DNA REMARK 1 REF EMBO J. V. 20 1449 2001 REMARK 1 REFN ISSN 0261-4189
REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 7204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 790 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 494 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 497 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.319 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 600 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 222 ; 0.011 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 935 ; 2.258 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 577 ; 1.758 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 262 ; 0.033 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 51 ; 0.009 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 4 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7081 13.6139 12.0936 REMARK 3 T TENSOR REMARK 3 T11: 0.0458 T22: 0.0215 REMARK 3 T33: 0.1022 T12: -0.0035 REMARK 3 T13: -0.0325 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 4.0121 L22: -0.1358 REMARK 3 L33: 4.7394 L12: 0.2340 REMARK 3 L13: 1.3187 L23: 2.0399 REMARK 3 S TENSOR REMARK 3 S11: 0.0280 S12: -0.2811 S13: 0.2197 REMARK 3 S21: -0.0433 S22: 0.0556 S23: 0.3215 REMARK 3 S31: 0.1066 S32: -0.1312 S33: -0.0836 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 8 REMARK 3 ORIGIN FOR THE GROUP (A): -7.6111 13.1846 -0.1169 REMARK 3 T TENSOR REMARK 3 T11: 0.1382 T22: 0.0490 REMARK 3 T33: 0.0262 T12: 0.0242 REMARK 3 T13: -0.0532 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 6.4446 L22: -0.5402 REMARK 3 L33: -0.4629 L12: 2.2701 REMARK 3 L13: 0.4938 L23: 0.1638 REMARK 3 S TENSOR REMARK 3 S11: -0.0506 S12: 0.4410 S13: -0.2029 REMARK 3 S21: 0.0665 S22: -0.0382 S23: -0.1387 REMARK 3 S31: -0.3612 S32: 0.0641 S33: 0.0888 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 12 REMARK 3 ORIGIN FOR THE GROUP (A): -15.4098 25.9671 -0.9276 REMARK 3 T TENSOR REMARK 3 T11: 0.0506 T22: 0.0436 REMARK 3 T33: 0.0468 T12: 0.0272 REMARK 3 T13: -0.0117 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: -0.3137 L22: 1.6817 REMARK 3 L33: 1.1623 L12: 0.7032 REMARK 3 L13: 0.0757 L23: -0.9843 REMARK 3 S TENSOR REMARK 3 S11: 0.1290 S12: 0.1562 S13: 0.1391 REMARK 3 S21: -0.0440 S22: 0.0034 S23: 0.2027 REMARK 3 S31: 0.1525 S32: 0.1452 S33: -0.1324 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 13 B 16 REMARK 3 ORIGIN FOR THE GROUP (A): -6.3763 25.3310 1.5435 REMARK 3 T TENSOR REMARK 3 T11: 0.0331 T22: 0.0665 REMARK 3 T33: 0.0134 T12: 0.0447 REMARK 3 T13: -0.0092 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 1.5853 L22: 2.6379 REMARK 3 L33: 3.7920 L12: 1.2601 REMARK 3 L13: -2.6557 L23: -1.0849 REMARK 3 S TENSOR REMARK 3 S11: 0.1100 S12: -0.0491 S13: -0.0959 REMARK 3 S21: 0.0231 S22: -0.0876 S23: -0.1814 REMARK 3 S31: 0.0696 S32: 0.0606 S33: -0.0224 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 17 B 20 REMARK 3 ORIGIN FOR THE GROUP (A): -12.5179 13.0635 8.3245 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: 0.0418 REMARK 3 T33: 0.0029 T12: 0.0183 REMARK 3 T13: -0.0240 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 0.1213 L22: 4.7512 REMARK 3 L33: -0.8892 L12: 0.2906 REMARK 3 L13: -0.0637 L23: -0.0916 REMARK 3 S TENSOR REMARK 3 S11: 0.1171 S12: -0.0688 S13: -0.0516 REMARK 3 S21: 0.1499 S22: -0.0524 S23: -0.0211 REMARK 3 S31: -0.0087 S32: -0.0016 S33: -0.0647 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 21 B 24 REMARK 3 ORIGIN FOR THE GROUP (A): 2.2069 5.5244 9.1375 REMARK 3 T TENSOR REMARK 3 T11: 0.0635 T22: 0.0389 REMARK 3 T33: 0.0469 T12: 0.0136 REMARK 3 T13: -0.0538 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 3.8040 L22: -0.2947 REMARK 3 L33: 0.9694 L12: 0.9477 REMARK 3 L13: 1.3796 L23: -0.4548 REMARK 3 S TENSOR REMARK 3 S11: -0.0221 S12: 0.0664 S13: -0.2537 REMARK 3 S21: 0.0465 S22: 0.1232 S23: 0.0877 REMARK 3 S31: -0.0193 S32: 0.1382 S33: -0.1010 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGEN ATOMS WERE ADDED IN THE RIDING REMARK 3 POSITIONS
REMARK 4 REMARK 4 3SSF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-11. REMARK 100 THE RCSB ID CODE IS RCSB066594.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8010 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8012 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 41.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.851 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1PJO REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% MPD, 0.04M HEXAMMINECOBALT(III) REMARK 280 CHLORIDE, 0.02M MAGNESIUM CHLORIDE, 0.04M LITHIUM CHLORIDE, 0.04M REMARK 280 SODIUM CACODYLATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.16000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.08000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.08000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.16000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 73 LIES ON A SPECIAL POSITION.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 U A 1 N1 U A 1 C6 0.059 REMARK 500 A A 3 C6 A A 3 N1 0.048 REMARK 500 G A 6 C2' G A 6 C1' -0.054 REMARK 500 A A 9 O5' A A 9 C5' -0.056 REMARK 500 G A 11 C5 G A 11 N7 -0.039 REMARK 500 DC B 14 N1 DC B 14 C6 0.044 REMARK 500 DT B 18 O3' DT B 18 C3' -0.039 REMARK 500 DT B 18 C2 DT B 18 N3 -0.058 REMARK 500 DT B 18 C5 DT B 18 C6 -0.042 REMARK 500 DT B 21 C6 DT B 21 N1 0.050 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 A A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 6 C3' - C2' - C1' ANGL. DEV. = -4.6 DEGREES REMARK 500 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 A A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 13 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 DT B 16 C4 - C5 - C7 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 17 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 18 O4' - C1' - C2' ANGL. DEV. = 5.2 DEGREES REMARK 500 DT B 18 N3 - C4 - O4 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT B 18 C5 - C4 - O4 ANGL. DEV. = -6.4 DEGREES REMARK 500 DT B 18 C4 - C5 - C7 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DC B 19 N3 - C4 - C5 ANGL. DEV. = -2.9 DEGREES REMARK 500 DC B 19 C4 - C5 - C6 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA B 24 O5' - P - OP2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA B 24 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DA B 24 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DA B 24 N1 - C2 - N3 ANGL. DEV. = -3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 A A 2 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 14 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 46 O REMARK 620 2 HOH A 57 O 167.8 REMARK 620 3 HOH A 44 O 87.6 103.5 REMARK 620 4 HOH A 45 O 96.6 88.4 89.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 56 O REMARK 620 2 HOH B 69 O 176.4 REMARK 620 3 HOH B 59 O 91.2 87.0 REMARK 620 4 HOH B 42 O 89.6 87.2 85.0 REMARK 620 5 HOH B 43 O 86.9 96.2 90.6 174.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 13 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 64 O REMARK 620 2 HOH A 63 O 91.0 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 14
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PJO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN RNA/DNA HYBRID OF HIV-1 PPT REMARK 900 RELATED ID: 1PJG RELATED DB: PDB REMARK 900 RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG REMARK 900 RELATED ID: 1JB8 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF AN RNA/DNA HYBRID REVEALS NOVEL REMARK 900 INTERMOLECULAR INTERCALATION REMARK 900 RELATED ID: 1G4Q RELATED DB: PDB REMARK 900 RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG
DBREF 3SSF A 1 12 PDB 3SSF 3SSF 1 12 DBREF 3SSF B 13 24 PDB 3SSF 3SSF 13 24
SEQRES 1 A 12 U A A A A G A A A A G G SEQRES 1 B 12 DC DC DT DT DT DT DC DT DT DT DT DA
HET MG A 13 1 HET MG A 14 1 HET MG B 1 1
HETNAM MG MAGNESIUM ION
FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *76(H2 O)
LINK MG MG A 14 O HOH A 46 1555 1555 1.73 LINK MG MG B 1 O HOH B 56 1555 1555 1.83 LINK MG MG A 14 O HOH A 57 1555 1555 1.85 LINK MG MG A 14 O HOH A 44 1555 1555 1.86 LINK MG MG A 13 O HOH A 64 1555 1555 1.94 LINK MG MG A 13 O HOH A 63 1555 1555 1.98 LINK MG MG B 1 O HOH B 69 1555 1555 1.99 LINK MG MG B 1 O HOH B 59 1555 1555 1.99 LINK MG MG B 1 O HOH B 42 1555 1555 2.00 LINK MG MG A 14 O HOH A 45 1555 1555 2.03 LINK MG MG B 1 O HOH B 43 1555 1555 2.05
SITE 1 AC1 2 HOH A 63 HOH A 64 SITE 1 AC2 5 HOH B 42 HOH B 43 HOH B 56 HOH B 59 SITE 2 AC2 5 HOH B 69 SITE 1 AC3 4 HOH A 44 HOH A 45 HOH A 46 HOH A 57
CRYST1 41.904 41.904 57.240 90.00 90.00 120.00 P 32 2 1 6
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.023864 0.013778 0.000000 0.00000
SCALE2 0.000000 0.027556 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017470 0.00000