PDB Short entry for 1L6N HEADER VIRAL PROTEIN 11-MAR-02 1L6N TITLE STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG TITLE 2 POLYPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-283; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P11A KEYWDS GAG, MATRIX, CAPSID, MATURATION, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.TANG,Y.NDASSA,M.F.SUMMERS REVDAT 3 23-FEB-22 1L6N 1 REMARK SEQADV REVDAT 2 24-FEB-09 1L6N 1 VERSN REVDAT 1 26-JUN-02 1L6N 0 JRNL AUTH C.TANG,Y.NDASSA,M.F.SUMMERS JRNL TITL STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE JRNL TITL 2 IMMATURE HIV-1 GAG POLYPROTEIN. JRNL REF NAT.STRUCT.BIOL. V. 9 537 2002 JRNL REFN ISSN 1072-8368 JRNL PMID 12032547 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, DYANA 1.5 REMARK 3 AUTHORS : GUENTERT (DYANA), GUENTERT,P., MUMENTHALER,C., & REMARK 3 WUTHRICH,K. (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED REMARK 3 USING DYANA 1.5 AND REMARK 3 THE STANDARD TORSION ANGLE SIMULATED ANNEALING PROTOCOL. REMARK 3 PRELIMINARY CALCULATIONS WERE REMARK 3 CARRIED OUT INDEPENDENTLY FOR MATRIX AND CAPSID N-TERMINAL DOMAINS REMARK 3 OF THE PROTEIN. REMARK 3 INITIALLY ONLY NOE DISTANCE CONSTRAINTS WERE IMPOSED. UNAMBIGUOUS REMARK 3 H-BONDS WERE ALSO REMARK 3 INCORPORATED TO REINFORCE CANONICAL SECONDARY STRUCTURE. THE REMARK 3 INITIAL STRUCTURES WERE REMARK 3 THEN USED TO ASSESS THE ACCURACY OF THE TORSION ANGLE CONSTRAINTS REMARK 3 GENERATED BY ANALYSIS REMARK 3 OF HA, CA, CB, CO AND N CHEMICAL SHIFTS WITH THE PROGRAM TALOS. REMARK 3 FINALLY, ALL THE REMARK 3 CONSTRAINTS WERE USED TO CALCULATE THE STRUCTURE OF THE WHOLE REMARK 3 PROTEIN. REMARK 4 REMARK 4 1L6N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015691. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM U-15N,13C GAG283, 50MM REMARK 210 ACETATE BUFFER(PH5.0), 100MM REMARK 210 NACL, 5MM BME; 1MM U-15N,13C REMARK 210 GAG283, 50MM ACETATE REMARK 210 BUFFER(PH5.0), 100MM NACL, 5MM REMARK 210 BME; 1MM U-15N,2H GAG283, 50MM REMARK 210 ACETATE BUFFER(PH5.0), 100MM REMARK 210 NACL, 5MM BME; 1MM U-15N GAG283, REMARK 210 50MM ACETATE BUFFER(PH5.0), REMARK 210 100MM NACL, 5MM BME REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C-SEPARATED_NOESY; REMARK 210 4D_13C/15N-SEPARATED_NOESY; 3D_ REMARK 210 15N-SEPARATED_NOESY; 4D_15N/15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.0, XWINNMR 2.6 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 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 O ALA A 100 H ILE A 104 1.48 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 ALA A 3 176.07 62.74 REMARK 500 1 ARG A 4 121.84 63.79 REMARK 500 1 SER A 6 94.99 -179.03 REMARK 500 1 VAL A 7 -66.86 -152.81 REMARK 500 1 LYS A 18 46.75 -86.60 REMARK 500 1 LEU A 21 -133.29 -65.46 REMARK 500 1 ALA A 45 34.10 74.37 REMARK 500 1 SER A 72 -177.15 167.54 REMARK 500 1 ARG A 91 48.84 71.52 REMARK 500 1 LYS A 95 -46.75 -144.07 REMARK 500 1 ASP A 121 35.92 -92.36 REMARK 500 1 THR A 122 152.94 -38.29 REMARK 500 1 MET A 142 150.19 59.78 REMARK 500 1 LYS A 162 58.44 -165.09 REMARK 500 1 SER A 165 163.52 179.84 REMARK 500 1 VAL A 191 -179.44 -51.07 REMARK 500 1 HIS A 194 118.16 -171.64 REMARK 500 1 GLN A 227 160.24 -44.26 REMARK 500 1 ARG A 229 -179.97 -49.95 REMARK 500 1 THR A 280 78.02 38.82 REMARK 500 1 HIS A 285 141.99 -172.60 REMARK 500 2 ALA A 3 138.55 -178.50 REMARK 500 2 ALA A 5 -82.66 -125.70 REMARK 500 2 SER A 6 55.59 -176.24 REMARK 500 2 VAL A 7 -65.24 -154.94 REMARK 500 2 LYS A 18 39.31 -91.05 REMARK 500 2 LEU A 21 -137.68 -71.32 REMARK 500 2 ALA A 45 40.55 74.49 REMARK 500 2 ILE A 60 -71.90 -71.17 REMARK 500 2 SER A 72 -177.18 166.40 REMARK 500 2 ARG A 91 40.60 81.24 REMARK 500 2 LYS A 95 19.76 -147.58 REMARK 500 2 SER A 126 136.80 62.99 REMARK 500 2 GLN A 127 139.40 -172.74 REMARK 500 2 GLN A 139 164.97 67.71 REMARK 500 2 GLN A 141 91.66 64.55 REMARK 500 2 LYS A 162 -76.39 -129.47 REMARK 500 2 ALA A 163 -47.61 85.52 REMARK 500 2 VAL A 191 -176.33 -52.30 REMARK 500 2 HIS A 194 134.69 76.58 REMARK 500 2 HIS A 219 88.88 36.62 REMARK 500 2 ALA A 220 72.83 -69.37 REMARK 500 2 GLN A 227 71.33 -108.24 REMARK 500 2 MET A 228 86.50 -55.30 REMARK 500 2 GLU A 230 83.57 65.08 REMARK 500 2 HIS A 288 135.60 -175.76 REMARK 500 3 ALA A 3 -61.10 -174.82 REMARK 500 3 ARG A 4 -36.72 177.68 REMARK 500 3 LYS A 18 41.40 -92.61 REMARK 500 3 LEU A 21 -133.58 -73.20 REMARK 500 REMARK 500 THIS ENTRY HAS 595 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1L6N A 1 283 UNP Q72497 Q72497_9HIV1 1 283 SEQADV 1L6N HIS A 284 UNP Q72497 EXPRESSION TAG SEQADV 1L6N HIS A 285 UNP Q72497 EXPRESSION TAG SEQADV 1L6N HIS A 286 UNP Q72497 EXPRESSION TAG SEQADV 1L6N HIS A 287 UNP Q72497 EXPRESSION TAG SEQADV 1L6N HIS A 288 UNP Q72497 EXPRESSION TAG SEQADV 1L6N HIS A 289 UNP Q72497 EXPRESSION TAG SEQRES 1 A 289 MET GLY ALA ARG ALA SER VAL LEU SER GLY GLY GLU LEU SEQRES 2 A 289 ASP LYS TRP GLU LYS ILE ARG LEU ARG PRO GLY GLY LYS SEQRES 3 A 289 LYS GLN TYR LYS LEU LYS HIS ILE VAL TRP ALA SER ARG SEQRES 4 A 289 GLU LEU GLU ARG PHE ALA VAL ASN PRO GLY LEU LEU GLU SEQRES 5 A 289 THR SER GLU GLY CYS ARG GLN ILE LEU GLY GLN LEU GLN SEQRES 6 A 289 PRO SER LEU GLN THR GLY SER GLU GLU LEU ARG SER LEU SEQRES 7 A 289 TYR ASN THR ILE ALA VAL LEU TYR CYS VAL HIS GLN ARG SEQRES 8 A 289 ILE ASP VAL LYS ASP THR LYS GLU ALA LEU ASP LYS ILE SEQRES 9 A 289 GLU GLU GLU GLN ASN LYS SER LYS LYS LYS ALA GLN GLN SEQRES 10 A 289 ALA ALA ALA ASP THR GLY ASN ASN SER GLN VAL SER GLN SEQRES 11 A 289 ASN TYR PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL SEQRES 12 A 289 HIS GLN ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL SEQRES 13 A 289 LYS VAL VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE SEQRES 14 A 289 PRO MET PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN SEQRES 15 A 289 ASP LEU ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN SEQRES 16 A 289 ALA ALA MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU SEQRES 17 A 289 ALA ALA GLU TRP ASP ARG LEU HIS PRO VAL HIS ALA GLY SEQRES 18 A 289 PRO ILE ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER SEQRES 19 A 289 ASP ILE ALA GLY THR THR SER THR LEU GLN GLU GLN ILE SEQRES 20 A 289 GLY TRP MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU SEQRES 21 A 289 ILE TYR LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE SEQRES 22 A 289 VAL ARG MET TYR SER PRO THR SER ILE LEU HIS HIS HIS SEQRES 23 A 289 HIS HIS HIS HELIX 1 1 SER A 9 GLU A 17 1 9 HELIX 2 2 LYS A 30 PHE A 44 1 15 HELIX 3 3 ASN A 47 LEU A 51 5 5 HELIX 4 4 THR A 53 GLN A 63 1 11 HELIX 5 5 LEU A 64 GLN A 69 1 6 HELIX 6 6 SER A 72 ARG A 91 1 20 HELIX 7 7 ASP A 96 ASP A 121 1 26 HELIX 8 8 SER A 148 ALA A 163 1 16 HELIX 9 9 VAL A 168 SER A 176 1 9 HELIX 10 10 THR A 180 VAL A 191 1 12 HELIX 11 11 HIS A 194 HIS A 216 1 23 HELIX 12 12 ARG A 232 GLY A 238 1 7 HELIX 13 13 THR A 242 THR A 251 1 10 HELIX 14 14 PRO A 257 TYR A 277 1 21 CISPEP 1 ASN A 253 PRO A 254 1 -0.04 CISPEP 2 ASN A 253 PRO A 254 2 0.01 CISPEP 3 ASN A 253 PRO A 254 3 0.03 CISPEP 4 ASN A 253 PRO A 254 4 0.06 CISPEP 5 ASN A 253 PRO A 254 5 0.10 CISPEP 6 ASN A 253 PRO A 254 6 -0.03 CISPEP 7 ASN A 253 PRO A 254 7 0.03 CISPEP 8 ASN A 253 PRO A 254 8 0.02 CISPEP 9 ASN A 253 PRO A 254 9 0.01 CISPEP 10 ASN A 253 PRO A 254 10 0.06 CISPEP 11 ASN A 253 PRO A 254 11 0.10 CISPEP 12 ASN A 253 PRO A 254 12 0.01 CISPEP 13 ASN A 253 PRO A 254 13 -0.02 CISPEP 14 ASN A 253 PRO A 254 14 0.01 CISPEP 15 ASN A 253 PRO A 254 15 -0.06 CISPEP 16 ASN A 253 PRO A 254 16 -0.02 CISPEP 17 ASN A 253 PRO A 254 17 0.13 CISPEP 18 ASN A 253 PRO A 254 18 -0.06 CISPEP 19 ASN A 253 PRO A 254 19 -0.06 CISPEP 20 ASN A 253 PRO A 254 20 -0.06 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