HEADER RNA 30-APR-98 397D TITLE A 1.3 A RESOLUTION CRYSTAL STRUCTURE OF THE HIV-1 TRANS-ACTIVATION TITLE 2 RESPONSE REGION RNA STEM REVEALS A METAL ION-DEPENDENT BULGE TITLE 3 CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*CP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*G)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*GP*CP*UP*CP*UP*CP*UP*GP*GP*CP*CP*C)-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 DOUBLE HELIX, OVERHANGING BASES, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.A.IPPOLITO,T.A.STEITZ REVDAT 5 21-FEB-24 397D 1 REMARK LINK REVDAT 4 24-FEB-09 397D 1 VERSN REVDAT 3 01-APR-03 397D 1 JRNL REVDAT 2 18-NOV-98 397D 3 REMARK DBREF CRYST1 FORMUL REVDAT 2 2 3 JRNL REVDAT 1 11-SEP-98 397D 0 JRNL AUTH J.A.IPPOLITO,T.A.STEITZ JRNL TITL A 1.3-A RESOLUTION CRYSTAL STRUCTURE OF THE HIV-1 JRNL TITL 2 TRANS-ACTIVATION RESPONSE REGION RNA STEM REVEALS A METAL JRNL TITL 3 ION-DEPENDENT BULGE CONFORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 95 9819 1998 JRNL REFN ISSN 0027-8424 JRNL PMID 9707559 JRNL DOI 10.1073/PNAS.95.17.9819 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 3 CROSS-VALIDATION METHOD : R FREE 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) : 0.131 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.126 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.099 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1731 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17465 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)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 567 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 178 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 : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.025 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: NULL REMARK 4 REMARK 4 397D 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_1000178861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-97; NULL REMARK 200 TEMPERATURE (KELVIN) : 100.00; NULL REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : CHESS; ROTATING ANODE REMARK 200 BEAMLINE : A1; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K; RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06000 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 292.00K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 G A 21 C3' - C2' - C1' ANGL. DEV. = -4.4 DEGREES REMARK 500 G A 30 N9 - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 G A 30 O4' - C1' - N9 ANGL. DEV. = 14.9 DEGREES REMARK 500 C B 37 N3 - C4 - C5 ANGL. DEV. = -2.5 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 48 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 23 OP1 REMARK 620 2 C A 24 OP2 89.3 REMARK 620 3 G A 26 OP2 94.0 107.3 REMARK 620 4 HOH A 52 O 177.1 89.7 83.7 REMARK 620 5 HOH A 53 O 93.3 84.1 166.5 89.3 REMARK 620 6 HOH A 54 O 92.6 170.0 82.4 88.8 86.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 49 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 26 OP1 REMARK 620 2 HOH A 55 O 72.7 REMARK 620 3 HOH A 56 O 139.4 69.3 REMARK 620 4 HOH A 58 O 84.6 99.7 88.0 REMARK 620 5 HOH A 59 O 86.7 157.0 133.0 88.2 REMARK 620 6 HOH A 60 O 150.9 135.3 69.5 95.5 64.3 REMARK 620 7 HOH A 136 O 97.1 83.2 92.3 177.0 89.4 81.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 50 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 27 OP1 REMARK 620 2 HOH A 61 O 165.0 REMARK 620 3 HOH A 62 O 101.2 88.9 REMARK 620 4 HOH A 63 O 87.1 84.2 78.3 REMARK 620 5 HOH A 64 O 90.3 75.6 149.1 73.7 REMARK 620 6 HOH A 65 O 113.5 79.6 75.4 149.2 126.1 REMARK 620 7 HOH A 66 O 76.1 104.9 133.4 146.0 77.1 64.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 51 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 67 O REMARK 620 2 HOH A 68 O 66.0 REMARK 620 3 HOH A 69 O 93.5 73.5 REMARK 620 4 HOH A 70 O 79.4 128.6 71.9 REMARK 620 5 HOH A 71 O 144.9 148.5 102.6 76.4 REMARK 620 6 HOH A 189 O 81.5 132.9 144.6 72.7 67.3 REMARK 620 7 HOH A 210 O 97.2 88.2 152.8 134.6 82.5 62.2 REMARK 620 8 HOH B 162 O 146.4 81.5 84.9 130.8 67.0 118.0 72.4 REMARK 620 N 1 2 3 4 5 6 7 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 48 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 49 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 51 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 50 DBREF 397D A 16 30 PDB 397D 397D 16 30 DBREF 397D B 36 47 PDB 397D 397D 36 47 SEQRES 1 A 15 G G C C A G A U C U G A G SEQRES 2 A 15 C G SEQRES 1 B 12 G C U C U C U G G C C C HET CA A 48 1 HET CA A 49 1 HET CA A 51 1 HET CA A 50 1 HETNAM CA CALCIUM ION FORMUL 3 CA 4(CA 2+) FORMUL 7 HOH *178(H2 O) LINK OP1 U A 23 CA CA A 48 1555 1555 2.28 LINK OP2 C A 24 CA CA A 48 1555 1555 2.32 LINK OP2 G A 26 CA CA A 48 1555 1555 2.32 LINK OP1 G A 26 CA CA A 49 1555 1555 2.36 LINK OP1 A A 27 CA CA A 50 1555 1555 2.32 LINK CA CA A 48 O HOH A 52 1555 1555 2.42 LINK CA CA A 48 O HOH A 53 1555 1555 2.37 LINK CA CA A 48 O HOH A 54 1555 1555 2.36 LINK CA CA A 49 O HOH A 55 1555 1555 2.42 LINK CA CA A 49 O HOH A 56 1555 1555 2.41 LINK CA CA A 49 O HOH A 58 1555 1555 2.36 LINK CA CA A 49 O HOH A 59 1555 1555 2.48 LINK CA CA A 49 O HOH A 60 1555 1555 2.46 LINK CA CA A 49 O HOH A 136 1555 1555 2.33 LINK CA CA A 50 O HOH A 61 1555 1555 2.34 LINK CA CA A 50 O HOH A 62 1555 1555 2.37 LINK CA CA A 50 O HOH A 63 1555 1555 2.44 LINK CA CA A 50 O HOH A 64 1555 1555 2.38 LINK CA CA A 50 O HOH A 65 1555 1555 2.49 LINK CA CA A 50 O HOH A 66 1555 1555 2.44 LINK CA CA A 51 O HOH A 67 1555 1555 2.42 LINK CA CA A 51 O HOH A 68 1555 1555 2.41 LINK CA CA A 51 O HOH A 69 1555 1555 2.42 LINK CA CA A 51 O HOH A 70 1555 1555 2.51 LINK CA CA A 51 O HOH A 71 1555 1555 2.47 LINK CA CA A 51 O HOH A 189 1555 1555 2.47 LINK CA CA A 51 O HOH A 210 1555 1555 2.17 LINK CA CA A 51 O HOH B 162 1555 1555 2.66 SITE 1 AC1 6 U A 23 C A 24 G A 26 HOH A 52 SITE 2 AC1 6 HOH A 53 HOH A 54 SITE 1 AC2 7 G A 26 HOH A 55 HOH A 56 HOH A 58 SITE 2 AC2 7 HOH A 59 HOH A 60 HOH A 136 SITE 1 AC3 8 HOH A 67 HOH A 68 HOH A 69 HOH A 70 SITE 2 AC3 8 HOH A 71 HOH A 189 HOH A 210 HOH B 162 SITE 1 AC4 7 A A 27 HOH A 61 HOH A 62 HOH A 63 SITE 2 AC4 7 HOH A 64 HOH A 65 HOH A 66 CRYST1 27.100 27.100 31.600 69.20 77.50 63.00 P 1 1 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 0.036900 -0.018802 -0.002752 0.00000 SCALE2 0.000000 0.041414 -0.012799 0.00000 SCALE3 0.000000 0.000000 0.033926 0.00000