HEADER DNA-RNA HYBRID 27-OCT-00 1G4Q TITLE RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYPURINE TRACT OF HIV-1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS RNA/DNA HYBRID, POLYPURINE TRACT OF HIV-1, DIRECT METHODS, DNA-RNA KEYWDS 2 COMPLEX, DNA-RNA HYBRID EXPDTA X-RAY DIFFRACTION AUTHOR G.W.HAN REVDAT 5 07-FEB-24 1G4Q 1 REMARK LINK REVDAT 4 04-OCT-17 1G4Q 1 REMARK REVDAT 3 24-FEB-09 1G4Q 1 VERSN REVDAT 2 09-MAR-04 1G4Q 1 JRNL REVDAT 1 08-JUL-03 1G4Q 0 JRNL AUTH G.W.HAN JRNL TITL DIRECT-METHODS DETERMINATION OF AN RNA/DNA HYBRID DECAMER AT JRNL TITL 2 1.15 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 213 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11173466 JRNL DOI 10.1107/S0907444900017595 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 PMID 14636594 REMARK 1 DOI 10.1016/J.JMB.2003.09.057 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.143 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 864 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 16408 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.140 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 805 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 15321 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 414 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4330 REMARK 3 NUMBER OF RESTRAINTS : 11665 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.019 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: KONNERT-HENDRICKSON CONJUGATE-GRADIENT REMARK 3 ALGORITHM REMARK 4 REMARK 4 1G4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000012230. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 9.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08100 REMARK 200 R SYM FOR SHELL (I) : 0.42400 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: DIRECT METHODS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CALCIUM ACETATE, SPERMIDINE, BETA REMARK 280 -OCTAGLUCOSIDE, MPD, SODIUM CACODYLATE, PH 6.8, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 12.84950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.05650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.53350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.05650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.84950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.53350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 A A 2 C2' A A 2 C1' 0.070 REMARK 500 G A 10 C2' G A 10 C1' 0.069 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 C A 1 N1 - C1' - C2' ANGL. DEV. = 10.2 DEGREES REMARK 500 C A 1 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 C A 1 C5 - C4 - N4 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 2 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 A A 2 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 A A 2 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 A A 6 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 A A 8 C6 - N1 - C2 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 8 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES REMARK 500 G A 10 N9 - C1' - C2' ANGL. DEV. = -9.1 DEGREES REMARK 500 G A 10 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES 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 CA A 31 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 9 OP1 REMARK 620 2 HOH A 111 O 84.1 REMARK 620 3 HOH A 113 O 99.0 83.0 REMARK 620 4 HOH A 115 O 83.9 93.1 174.8 REMARK 620 5 HOH A 118 O 171.2 87.7 83.1 93.3 REMARK 620 6 DT B 18 OP2 90.9 172.3 91.9 92.4 97.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 33 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 9 OP2 REMARK 620 2 HOH A 163 O 87.3 REMARK 620 3 HOH A 164 O 85.3 93.1 REMARK 620 4 HOH A 166 O 172.3 94.7 87.2 REMARK 620 5 HOH A 167 O 89.3 176.6 87.0 88.7 REMARK 620 6 HOH A 168 O 93.9 90.4 176.3 93.5 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 34 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 10 OP1 REMARK 620 2 HOH A 105 O 88.4 REMARK 620 3 HOH A 112 O 81.1 109.6 REMARK 620 4 HOH A 176 O 159.9 93.2 79.5 REMARK 620 5 DT B 18 OP1 91.4 161.5 88.6 93.4 REMARK 620 6 DG B 20 OP1 72.0 87.5 147.7 128.1 74.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 31 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 33 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 34 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 25 DBREF 1G4Q A 1 10 PDB 1G4Q 1G4Q 1 10 DBREF 1G4Q B 11 20 PDB 1G4Q 1G4Q 11 20 SEQRES 1 A 10 C A A A G A A A A G SEQRES 1 B 10 DC DT DT DT DT DC DT DT DT DG HET CA A 31 1 HET CA A 33 1 HET CA A 34 1 HET MPD A 25 8 HETNAM CA CALCIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 CA 3(CA 2+) FORMUL 6 MPD C6 H14 O2 FORMUL 7 HOH *137(H2 O) LINK OP1 A A 9 CA CA A 31 1555 1555 2.20 LINK OP2 A A 9 CA CA A 33 1555 1555 2.02 LINK OP1 G A 10 CA CA A 34 1555 1555 2.18 LINK CA CA A 31 O HOH A 111 1555 1555 2.28 LINK CA CA A 31 O HOH A 113 1555 1555 2.26 LINK CA CA A 31 O HOH A 115 1555 1555 2.29 LINK CA CA A 31 O HOH A 118 1555 1555 2.32 LINK CA CA A 31 OP2 DT B 18 1555 3646 2.25 LINK CA CA A 33 O HOH A 163 1555 1555 2.04 LINK CA CA A 33 O HOH A 164 1555 1555 2.13 LINK CA CA A 33 O HOH A 166 1555 1555 1.99 LINK CA CA A 33 O HOH A 167 1555 1555 2.16 LINK CA CA A 33 O HOH A 168 1555 1555 2.07 LINK CA CA A 34 O HOH A 105 1555 2555 2.43 LINK CA CA A 34 O HOH A 112 1555 1555 2.46 LINK CA CA A 34 O HOH A 176 1555 1555 2.31 LINK CA CA A 34 OP1 DT B 18 1555 3646 2.23 LINK CA CA A 34 OP1 DG B 20 1555 2555 2.90 SITE 1 AC1 6 A A 9 HOH A 111 HOH A 113 HOH A 115 SITE 2 AC1 6 HOH A 118 DT B 18 SITE 1 AC2 6 A A 9 HOH A 163 HOH A 164 HOH A 166 SITE 2 AC2 6 HOH A 167 HOH A 168 SITE 1 AC3 6 G A 10 HOH A 105 HOH A 112 HOH A 176 SITE 2 AC3 6 DT B 18 DG B 20 SITE 1 AC4 8 A A 4 G A 5 A A 6 HOH A 107 SITE 2 AC4 8 HOH A 208 HOH A 211 HOH A 238 HOH B 133 CRYST1 25.699 41.067 46.113 90.00 90.00 90.00 P 21 21 21 4 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 0.038912 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021686 0.00000