HEADER HYDROLASE 25-APR-02 1LKU OBSLTE 18-FEB-03 1LKU 1O1W TITLE SOLUTION STRUCTURE OF THE RNASE H DOMAIN OF THE HIV-1 TITLE 2 REVERSE TRANSCRIPTASE IN THE PRESENCE OF MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 VARIANT: STRAIN HXB2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BLR KEYWDS HIV-1, RNASE H DOMAIN, HIV-1 REVERSE TRANSCRIPTASE, KEYWDS 2 SOLUTION STRUCTURE, METAL BINDING EXPDTA NMR, 14 STRUCTURES AUTHOR K.PARI,G.A.MUELLER,E.F.DEROSE,T.W.KIRBY,R.E.LONDON REVDAT 2 18-FEB-03 1LKU 1 OBSLTE REVDAT 1 11-FEB-03 1LKU 0 JRNL AUTH K.PARI,G.A.MUELLER,E.F.DEROSE,T.W.KIRBY,R.E.LONDON JRNL TITL SOLUTION STRUCTURE OF THE RNASE H DOMAIN OF THE JRNL TITL 2 HIV-1 REVERSE TRANSCRIPTASE IN THE PRESENCE OF JRNL TITL 3 MAGNESIUM JRNL REF BIOCHEMISTRY V. 42 639 2003 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LKU COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-2002. REMARK 100 THE RCSB ID CODE IS RCSB016036. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM RNASE H U-15N, 13C; 10 REMARK 210 MM TRIS, PH6.8; 90% H20, 10% REMARK 210 D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 1.0, NMRPIPE 2.1, REMARK 210 NMRVIEW 5.0.4 REMARK 210 METHOD USED : AUTOMATED STRUCTURE REMARK 210 DETERMINATION WITH ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D REMARK 210 HETERONUCLEAR TECHNIQUES. 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: 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 3 PHE A 18 CE1 PHE A 18 CZ -0.041 REMARK 500 3 PHE A 18 CZ PHE A 18 CE2 0.039 REMARK 500 3 ILE A 73 CA ILE A 73 CB 0.024 REMARK 500 8 TYR A 5 CE1 TYR A 5 CZ -0.064 REMARK 500 8 TYR A 5 CZ TYR A 5 CE2 0.063 REMARK 500 10 TYR A 5 CE1 TYR A 5 CZ -0.034 REMARK 500 10 TYR A 5 CZ TYR A 5 CE2 0.036 REMARK 500 12 PHE A 18 CE1 PHE A 18 CZ -0.043 REMARK 500 12 PHE A 18 CZ PHE A 18 CE2 0.046 REMARK 500 13 TYR A 5 CE1 TYR A 5 CZ -0.031 REMARK 500 13 TYR A 5 CZ TYR A 5 CE2 0.030 REMARK 500 13 PHE A 18 CE1 PHE A 18 CZ -0.026 REMARK 500 13 PHE A 18 CZ PHE A 18 CE2 0.025 REMARK 500 13 TYR A 61 CE1 TYR A 61 CZ 0.022 REMARK 500 14 GLN A 42 C GLN A 42 O -0.024 REMARK 500 14 TYR A 61 CE1 TYR A 61 CZ -0.045 REMARK 500 14 TYR A 61 CZ TYR A 61 CE2 0.044 REMARK 500 14 GLN A 85 CA GLN A 85 C -0.022 REMARK 500 14 ALA A 86 N ALA A 86 CA -0.021 REMARK 500 14 ALA A 86 CA ALA A 86 CB -0.023 REMARK 500 14 GLN A 87 CA GLN A 87 C 0.023 REMARK 500 14 ALA A 86 C GLN A 87 N -0.031 REMARK 500 14 GLN A 87 C PRO A 88 N 0.037 REMARK 500 14 TYR A 110 CE1 TYR A 110 CZ -0.020 REMARK 500 14 TYR A 110 CZ TYR A 110 CE2 0.021 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ASP A 76 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 2 GLN A 78 N - CA - C ANGL. DEV. = -4.0 DEGREES REMARK 500 3 GLN A 78 N - CA - C ANGL. DEV. = -3.7 DEGREES REMARK 500 4 ASP A 76 N - CA - C ANGL. DEV. = -3.8 DEGREES REMARK 500 4 GLN A 78 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 5 GLN A 78 N - CA - C ANGL. DEV. = -3.3 DEGREES REMARK 500 6 GLN A 78 N - CA - C ANGL. DEV. = -4.1 DEGREES REMARK 500 8 TYR A 5 OH - CZ - CE2 ANGL. DEV. = -4.6 DEGREES REMARK 500 8 TYR A 5 CE1 - CZ - OH ANGL. DEV. = 4.6 DEGREES REMARK 500 8 GLN A 78 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 9 ASP A 76 N - CA - C ANGL. DEV. = -4.0 DEGREES REMARK 500 10 TYR A 19 N - CA - CB ANGL. DEV. = -3.9 DEGREES REMARK 500 10 TYR A 19 C - N - CA ANGL. DEV. = 3.4 DEGREES REMARK 500 10 GLN A 78 N - CA - C ANGL. DEV. = -3.9 DEGREES REMARK 500 11 GLN A 78 N - CA - C ANGL. DEV. = -3.7 DEGREES REMARK 500 12 ASP A 76 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 12 GLN A 78 N - CA - C ANGL. DEV. = -4.0 DEGREES REMARK 500 13 LEU A 64 CB - CA - C ANGL. DEV. = 3.8 DEGREES REMARK 500 13 GLN A 78 N - CA - C ANGL. DEV. = -3.8 DEGREES REMARK 500 14 LYS A 43 CA - CB - CG ANGL. DEV. = -3.9 DEGREES REMARK 500 14 TYR A 61 OH - CZ - CE2 ANGL. DEV. = -3.3 DEGREES REMARK 500 14 GLN A 78 N - CA - C ANGL. DEV. = -4.0 DEGREES REMARK 500 14 GLN A 87 N - CA - CB ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ALA A 86 CA - C - N ANGL. DEV. = -6.0 DEGREES REMARK 500 14 ALA A 86 O - C - N ANGL. DEV. = 3.3 DEGREES REMARK 500 14 GLN A 87 C - N - CA ANGL. DEV. = 5.6 DEGREES REMARK 500 14 GLN A 87 CA - C - N ANGL. DEV. = 3.4 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 1 GLU A 3 127.01 65.72 REMARK 500 1 VAL A 13 -83.37 60.64 REMARK 500 2 VAL A 13 -87.80 57.72 REMARK 500 2 GLU A 124 -118.72 56.86 REMARK 500 3 VAL A 13 -80.41 65.22 REMARK 500 3 GLN A 90 123.02 66.75 REMARK 500 3 SER A 131 142.45 65.70 REMARK 500 3 ARG A 135 139.22 65.56 REMARK 500 4 GLN A 90 123.16 62.14 REMARK 500 4 ILE A 120 -82.87 64.87 REMARK 500 4 VAL A 126 134.49 67.70 REMARK 500 5 GLU A 3 -98.59 57.46 REMARK 500 5 VAL A 13 -41.42 76.08 REMARK 500 5 GLN A 90 123.80 64.51 REMARK 500 5 ALA A 116 -100.50 55.75 REMARK 500 6 VAL A 13 -80.12 67.36 REMARK 500 6 ALA A 116 -99.95 55.09 REMARK 500 6 GLU A 124 -87.18 63.88 REMARK 500 7 VAL A 13 -85.10 61.41 REMARK 500 7 GLN A 90 132.58 67.74 REMARK 500 7 GLU A 92 -92.38 33.20 REMARK 500 7 ASP A 127 -75.63 67.52 REMARK 500 8 VAL A 13 -86.13 60.89 REMARK 500 8 GLN A 90 121.23 64.81 REMARK 500 8 LEU A 129 154.89 66.03 REMARK 500 9 GLU A 124 -90.31 59.05 REMARK 500 10 GLU A 3 122.91 64.77 REMARK 500 10 VAL A 13 -80.27 63.77 REMARK 500 10 GLN A 125 -53.23 74.55 REMARK 500 11 ASN A 2 -140.65 159.24 REMARK 500 11 VAL A 13 -76.98 68.03 REMARK 500 12 VAL A 13 -86.78 61.59 REMARK 500 12 SER A 131 -94.76 56.96 REMARK 500 12 ARG A 135 -100.09 56.48 REMARK 500 13 VAL A 13 -51.51 76.56 REMARK 500 13 GLN A 90 124.52 63.67 REMARK 500 13 GLN A 125 127.05 64.63 REMARK 500 14 VAL A 13 -84.67 62.37 REMARK 500 14 ALA A 86 121.98 53.99 REMARK 500 14 GLU A 92 -92.49 47.79 REMARK 500 14 LEU A 129 153.99 63.80 DBREF 1LKU A 5 138 UNP P04585 POL_HV1H2 582 715 SEQADV 1LKU MET A 1 UNP P04585 CLONING ARTIFACT SEQADV 1LKU ASN A 2 UNP P04585 CLONING ARTIFACT SEQADV 1LKU GLU A 3 UNP P04585 CLONING ARTIFACT SEQADV 1LKU LEU A 4 UNP P04585 CLONING ARTIFACT SEQRES 1 A 138 MET ASN GLU LEU TYR GLN LEU GLU LYS GLU PRO ILE VAL SEQRES 2 A 138 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA ALA ASN ARG SEQRES 3 A 138 GLU THR LYS LEU GLY LYS ALA GLY TYR VAL THR ASN ARG SEQRES 4 A 138 GLY ARG GLN LYS VAL VAL THR LEU THR ASP THR THR ASN SEQRES 5 A 138 GLN LYS THR GLU LEU GLN ALA ILE TYR LEU ALA LEU GLN SEQRES 6 A 138 ASP SER GLY LEU GLU VAL ASN ILE VAL THR ASP SER GLN SEQRES 7 A 138 TYR ALA LEU GLY ILE ILE GLN ALA GLN PRO ASP GLN SER SEQRES 8 A 138 GLU SER GLU LEU VAL ASN GLN ILE ILE GLU GLN LEU ILE SEQRES 9 A 138 LYS LYS GLU LYS VAL TYR LEU ALA TRP VAL PRO ALA HIS SEQRES 10 A 138 LYS GLY ILE GLY GLY ASN GLU GLN VAL ASP LYS LEU VAL SEQRES 11 A 138 SER ALA GLY ILE ARG LYS VAL LEU HELIX 1 1 THR A 51 LEU A 64 1 14 HELIX 2 2 SER A 77 GLN A 85 1 9 HELIX 3 3 SER A 93 LYS A 106 1 14 SHEET 1 A 5 ARG A 41 THR A 46 0 SHEET 2 A 5 LYS A 32 THR A 37 -1 N ALA A 33 O VAL A 45 SHEET 3 A 5 THR A 17 VAL A 20 -1 N TYR A 19 O VAL A 36 SHEET 4 A 5 GLU A 70 VAL A 74 1 O ASN A 72 N PHE A 18 SHEET 5 A 5 LYS A 108 ALA A 112 1 O LYS A 108 N VAL A 71 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 MODEL 1