10 20 30 40 50 60 70 80 2A9X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA BINDING PROTEIN/RNA 12-JUL-05 2A9X
TITLE TAR RNA RECOGNITION BY A CYCLIC PEPTIDOMIMETIC OF TAT TITLE 2 PROTEIN
CAVEAT 2A9X CHIRALITY ERROR AT CA CENTER OF PRO 13
COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIV-2 CYCLIC PEPTIDE; COMPND 3 CHAIN: 1; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BIV TAR RNA; COMPND 7 CHAIN: 2; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE BIV-2 PEPTIDE WAS SYNTHESIZED BY SOLID SOURCE 4 PHASE SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: RNA WAS TRANSCRIBED IN VITRO FROM DNA SOURCE 8 OLIGONUCLEOTIDE TEMPLATES WITH T7 RNA POLYMERASE PURIFIED SOURCE 9 IN HOUSE WITH UNLABELED OR 13C/15N ENRICHED NTPS SOURCE 10 (SILANTES) AND PURIFIED BY DENATURING PAGE.
KEYWDS NMR; PEPTIDOMIMETICS; PEPTIDE STRUCTURE, RNA RECOGNITION; KEYWDS 2 IMMUNODEFICIENCY VIRUS; TAR RNA;, RNA BINDING PROTEIN/RNA KEYWDS 3 COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR T.C.LEEPER,Z.ATHANASSIOU,R.L.DIAS,J.A.ROBINSON,G.VARANI
REVDAT 2 24-FEB-09 2A9X 1 VERSN REVDAT 1 01-NOV-05 2A9X 0
JRNL AUTH T.C.LEEPER,Z.ATHANASSIOU,R.L.DIAS,J.A.ROBINSON, JRNL AUTH 2 G.VARANI JRNL TITL TAR RNA RECOGNITION BY A CYCLIC PEPTIDOMIMETIC OF JRNL TITL 2 TAT PROTEIN. JRNL REF BIOCHEMISTRY V. 44 12362 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16156649 JRNL DOI 10.1021/BI0510532
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.9 REMARK 3 AUTHORS : SCHWIETERS ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2A9X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-05. REMARK 100 THE RCSB ID CODE IS RCSB033668.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 275 REMARK 210 PH : 5; 5 REMARK 210 IONIC STRENGTH : 20 MM NA+; 20 MM NA+ REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM BIV-2 PEPTIDE PLUS REMARK 210 UNLABELED 0.8 MM BIV TAR RNA, REMARK 210 20 MM SODIUM ACETATE, D3, PH REMARK 210 5.0, 100% D2O; 0.8 MM BIV-2 REMARK 210 PEPTIDE PLUS UNLABELED 0.8 MM REMARK 210 BIV TAR RNA, 20 MM SODIUM REMARK 210 ACETATE, D3, PH 5.0, 90% H2O, REMARK 210 10% D2O; 0.6 MM BIV-2 PEPTIDE REMARK 210 PLUS 13C/15N LABELED 0.6 MM REMARK 210 BIV TAR RNA, 20 MM SODIUM REMARK 210 ACETATE, D3, PH 5.0, 100% D2O; REMARK 210 0.6 MM BIV-2 PEPTIDE PLUS 13C/ REMARK 210 15N LABELED 0.6 MM BIV TAR REMARK 210 RNA, 20 MM SODIUM ACETATE, D3, REMARK 210 PH 5.0, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, HCCH-COSY, HCCH- REMARK 210 TOCSY, HNN-COSY, F1FF2F-TYPE REMARK 210 2D TOCSY, F1FF2F-TYPE 2D REMARK 210 NOESY, 3D 31P HETCOR ETC, IPAP REMARK 210 -HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX, DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.0, NMRPIPE 2.3, X- REMARK 210 PLOR 2.9, SPARKY 3.110 REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 U 2 16 C5 C 2 17 1.96 REMARK 500 O2' C 2 17 O5' A 2 18 2.14 REMARK 500 O2' U 2 16 O5' C 2 17 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 2 C 2 26 C4' C 2 26 C3' 0.067 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 1 G 2 11 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES REMARK 500 1 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.1 DEGREES REMARK 500 3 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.9 DEGREES REMARK 500 3 U 2 16 C5' - C4' - C3' ANGL. DEV. = -8.9 DEGREES REMARK 500 3 A 2 21 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 4 U 2 10 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 4 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES REMARK 500 5 G 2 11 C5' - C4' - C3' ANGL. DEV. = -9.7 DEGREES REMARK 500 5 A 2 18 C5' - C4' - C3' ANGL. DEV. = -10.2 DEGREES REMARK 500 5 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.8 DEGREES REMARK 500 6 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 6 A 2 13 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 6 U 2 16 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 6 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.9 DEGREES REMARK 500 6 G 2 22 C5' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 7 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 8 A 2 13 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 8 U 2 16 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 8 A 2 18 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES REMARK 500 8 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.5 DEGREES REMARK 500 9 G 2 11 C5' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 9 U 2 16 C5' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 10 U 2 16 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 10 A 2 21 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ARG 1 3 1.18 -64.87 REMARK 500 1 THR 1 4 71.35 26.38 REMARK 500 1 ARG 1 5 149.54 -37.97 REMARK 500 1 LYS 1 7 -43.30 -141.18 REMARK 500 1 ARG 1 8 -159.01 -92.08 REMARK 500 1 PRO 1 13 -122.46 77.65 REMARK 500 2 VAL 1 2 60.91 -150.75 REMARK 500 2 ARG 1 5 101.18 -40.73 REMARK 500 2 PRO 1 13 -126.06 77.15 REMARK 500 3 THR 1 4 54.75 -63.62 REMARK 500 3 PRO 1 13 -121.59 73.67 REMARK 500 4 ARG 1 3 81.30 -55.51 REMARK 500 4 THR 1 4 81.41 -60.90 REMARK 500 4 ARG 1 5 -92.12 -39.34 REMARK 500 4 ARG 1 9 112.63 -165.10 REMARK 500 4 PRO 1 13 -102.38 48.88 REMARK 500 5 ARG 1 3 41.90 -101.90 REMARK 500 5 ARG 1 8 -158.30 -101.00 REMARK 500 5 PRO 1 13 -124.19 80.63 REMARK 500 6 VAL 1 2 84.73 -171.56 REMARK 500 6 ARG 1 8 -152.24 -134.92 REMARK 500 6 PRO 1 13 -127.84 82.58 REMARK 500 7 THR 1 4 85.02 -69.16 REMARK 500 7 ARG 1 5 -168.66 -58.68 REMARK 500 7 ARG 1 9 106.91 -161.29 REMARK 500 7 PRO 1 13 -128.84 84.93 REMARK 500 8 THR 1 4 89.78 -45.09 REMARK 500 8 ARG 1 5 -153.42 -64.80 REMARK 500 8 ARG 1 8 -155.42 -97.92 REMARK 500 8 ARG 1 9 91.87 -176.88 REMARK 500 8 VAL 1 12 86.79 -152.22 REMARK 500 8 PRO 1 13 -131.12 84.96 REMARK 500 9 ARG 1 3 53.37 -145.68 REMARK 500 9 ARG 1 8 -145.88 -94.73 REMARK 500 9 ARG 1 9 100.76 -165.73 REMARK 500 9 VAL 1 12 87.73 -154.42 REMARK 500 9 PRO 1 13 -135.32 81.30 REMARK 500 10 THR 1 4 2.25 -57.67 REMARK 500 10 ARG 1 5 23.62 39.13 REMARK 500 10 ARG 1 8 -155.66 -59.79 REMARK 500 10 ARG 1 9 113.63 -170.42 REMARK 500 10 PRO 1 13 -128.64 85.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 1 PRO 1 13 119.3 ALPHA-CARBON REMARK 500 2 PRO 1 13 119.3 ALPHA-CARBON REMARK 500 3 PRO 1 13 119.2 ALPHA-CARBON REMARK 500 4 PRO 1 13 119.2 ALPHA-CARBON REMARK 500 5 PRO 1 13 119.3 ALPHA-CARBON REMARK 500 6 PRO 1 13 119.3 ALPHA-CARBON REMARK 500 7 PRO 1 13 119.3 ALPHA-CARBON REMARK 500 8 PRO 1 13 119.3 ALPHA-CARBON REMARK 500 9 PRO 1 13 119.2 ALPHA-CARBON REMARK 500 10 PRO 1 13 119.3 ALPHA-CARBON REMARK 500 REMARK 500 REMARK: NULL
DBREF 2A9X 2 4 31 PDB 2A9X 2A9X 4 31 DBREF 2A9X 1 1 14 PDB 2A9X 2A9X 1 14
SEQRES 1 1 14 ARG VAL ARG THR ARG GLY LYS ARG ARG ILE ARG VAL PRO SEQRES 2 1 14 PRO SEQRES 1 2 28 G G C U C G U G U A G C U SEQRES 2 2 28 C A U U A G C U C C G A G SEQRES 3 2 28 C C
LINK N ARG 1 1 C PRO 1 14 1555 1555 1.31
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000