HEADER HYDROLASE 12-FEB-03 1O1W TITLE SOLUTION STRUCTURE OF THE RNASE H DOMAIN OF THE HIV-1 REVERSE TITLE 2 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 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 VARIANT: STRAIN HXB2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BLR KEYWDS HIV-1, RNASE H DOMAIN, HIV-1 REVERSE TRANSCRIPTASE, SOLUTION KEYWDS 2 STRUCTURE, METAL BINDING, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR K.PARI,G.A.MUELLER,E.F.DEROSE,T.W.KIRBY,R.E.LONDON REVDAT 4 27-DEC-23 1O1W 1 REMARK REVDAT 3 23-FEB-22 1O1W 1 REMARK SEQADV REVDAT 2 24-FEB-09 1O1W 1 VERSN REVDAT 1 18-FEB-03 1O1W 0 SPRSDE 18-FEB-03 1O1W 1LKU 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 HIV-1 JRNL TITL 2 REVERSE TRANSCRIPTASE IN THE PRESENCE OF MAGNESIUM JRNL REF BIOCHEMISTRY V. 42 639 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12534276 JRNL DOI 10.1021/BI0204894 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 1O1W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000001700. 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 MM REMARK 210 TRIS, PH6.8; 90% H20, 10% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_ 15N REMARK 210 -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, NMRVIEW REMARK 210 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 : 7 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 HG SER A 67 H GLY A 68 1.35 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 TYR A 19 CE1 TYR A 19 CZ 0.092 REMARK 500 2 TYR A 19 CZ TYR A 19 CE2 -0.095 REMARK 500 4 TYR A 35 CE1 TYR A 35 CZ -0.079 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 ASN A 2 -157.96 53.94 REMARK 500 1 TYR A 5 -179.46 173.36 REMARK 500 1 GLU A 8 -89.66 -110.69 REMARK 500 1 LYS A 9 0.50 59.19 REMARK 500 1 PRO A 11 122.17 -39.74 REMARK 500 1 LYS A 29 70.36 50.06 REMARK 500 1 LEU A 30 149.99 -173.09 REMARK 500 1 ALA A 33 118.59 -165.35 REMARK 500 1 ASN A 38 -4.40 -55.93 REMARK 500 1 LEU A 69 -85.99 -103.90 REMARK 500 1 SER A 77 108.44 -165.10 REMARK 500 1 ALA A 86 47.65 -90.22 REMARK 500 1 GLN A 87 70.53 32.85 REMARK 500 1 PRO A 88 32.76 -81.08 REMARK 500 1 GLN A 90 20.68 -163.78 REMARK 500 1 GLU A 92 -132.40 49.25 REMARK 500 1 SER A 93 144.66 -38.88 REMARK 500 1 GLU A 107 -80.77 -92.93 REMARK 500 1 PRO A 115 111.50 -38.16 REMARK 500 1 ALA A 116 -133.96 169.08 REMARK 500 1 HIS A 117 -1.96 -179.24 REMARK 500 1 ASP A 127 -72.29 -97.02 REMARK 500 1 LYS A 128 34.86 -161.72 REMARK 500 1 LEU A 129 79.68 55.79 REMARK 500 1 SER A 131 61.61 -109.14 REMARK 500 1 ILE A 134 53.52 -90.81 REMARK 500 1 ARG A 135 33.40 -141.34 REMARK 500 2 ASN A 2 -158.89 -99.58 REMARK 500 2 LEU A 4 -24.30 -148.69 REMARK 500 2 GLU A 8 -85.63 -120.58 REMARK 500 2 LYS A 9 3.75 57.49 REMARK 500 2 PRO A 11 103.65 -43.30 REMARK 500 2 ASP A 21 133.36 -171.62 REMARK 500 2 ASN A 25 100.69 -50.47 REMARK 500 2 ALA A 33 119.02 -164.50 REMARK 500 2 ASN A 38 -6.35 -55.43 REMARK 500 2 LEU A 69 -95.73 -132.13 REMARK 500 2 SER A 77 111.77 -165.66 REMARK 500 2 ALA A 86 47.30 -97.74 REMARK 500 2 GLN A 87 68.26 35.53 REMARK 500 2 PRO A 88 33.27 -82.87 REMARK 500 2 GLN A 90 21.14 -165.62 REMARK 500 2 GLU A 92 -121.94 52.09 REMARK 500 2 SER A 93 142.87 -37.92 REMARK 500 2 LYS A 108 166.81 162.16 REMARK 500 2 PRO A 115 111.68 -39.87 REMARK 500 2 ALA A 116 -160.49 178.52 REMARK 500 2 HIS A 117 46.86 -177.94 REMARK 500 2 ILE A 120 -85.46 -160.95 REMARK 500 2 ASN A 123 29.23 44.19 REMARK 500 REMARK 500 THIS ENTRY HAS 186 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1O1W A 5 138 UNP P04585 POL_HV1H2 582 715 SEQADV 1O1W MET A 1 UNP P04585 CLONING ARTIFACT SEQADV 1O1W ASN A 2 UNP P04585 CLONING ARTIFACT SEQADV 1O1W GLU A 3 UNP P04585 CLONING ARTIFACT SEQADV 1O1W 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