PDB Short entry for 1D8V HEADER ANTITUMOR PROTEIN 26-OCT-99 1D8V TITLE THE RESTRAINED AND MINIMIZED AVERAGE NMR STRUCTURE OF MAP30. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-HIV AND ANTI-TUMOR PROTEIN MAP30; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MOMORDICA CHARANTIA; SOURCE 3 ORGANISM_COMMON: BALSAM PEAR; SOURCE 4 ORGANISM_TAXID: 3673 KEYWDS SINGLE CHAIN, ANTITUMOR PROTEIN EXPDTA SOLUTION NMR AUTHOR Y.-X.WANG,N.NEAMATI,J.JACOB,I.PALMER,S.J.STAHL REVDAT 5 16-FEB-22 1D8V 1 REMARK SEQADV REVDAT 4 24-FEB-09 1D8V 1 VERSN REVDAT 3 01-APR-03 1D8V 1 JRNL REVDAT 2 10-MAY-00 1D8V 1 DBREF SEQADV REMARK REVDAT 1 19-NOV-99 1D8V 0 JRNL AUTH Y.X.WANG,N.NEAMATI,J.JACOB,I.PALMER,S.J.STAHL,J.D.KAUFMAN, JRNL AUTH 2 P.L.HUANG,P.L.HUANG,H.E.WINSLOW,Y.POMMIER,P.T.WINGFIELD, JRNL AUTH 3 S.LEE-HUANG,A.BAX,D.A.TORCHIA JRNL TITL SOLUTION STRUCTURE OF ANTI-HIV-1 AND ANTI-TUMOR PROTEIN JRNL TITL 2 MAP30: STRUCTURAL INSIGHTS INTO ITS MULTIPLE FUNCTIONS. JRNL REF CELL(CAMBRIDGE,MASS.) V. 99 433 1999 JRNL REFN ISSN 0092-8674 JRNL PMID 10571185 JRNL DOI 10.1016/S0092-8674(00)81529-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MODIFIED X-PLOR 3.5 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 WE CALCULATED THE STRUCTURE OF MAP30 USING SIMULATED ANNEALING IN REMARK 3 TORSION ANGLE SPACE STARTING FROM AN EXTENDED STRAND, FOLLOWED BY REMARK 3 SIMULATED ANEALING IN CARTESIAN SPACE USING A MODIFIED XPLOR 3.5, REMARK 3 CONTAINING PSEUDOPOTENTIALS FOR RESIDUAL DIPOLAR COUPLING AND A REMARK 3 CONFORMATIONAL DATABASE. HYDROGEN BOND CONSTRAINTS, TWO FOR EACH REMARK 3 HYDROGEN BOND (NH-O = 1.5-2.8 A AND N-O = 2.4-3.5 A), WERE DERIVED REMARK 3 FROM NH EXCHANGE EXPERIMENTS, BACKBONE NOE PATTERNS, BACKBONE CA/ REMARK 3 CB CHEMICAL SHIFTS AND DIRECT MEASUREMENTS OF 3HJNC CONNECTIVITY REMARK 3 ACROSS HYDROGEN BONDS, AND APPLIED IN THE LATER STAGE OF THE REMARK 3 STRUCTURE CALCULATION. PHI AND PSI ANGLES WERE DERIVED FROM THREE- REMARK 3 BOND 3JHNHA COUPLING CONSTANTS, REMARK 3 MEASURED WITH THE 3D HNHA EXPERIMENT AND A DATABASE ANALYSIS OF REMARK 3 BACKBONE (1H, 15N, 13CA, 13CB AND C) CHEMICAL SHIFTS, USING THE REMARK 3 PROGRAM TALOS. THE PHI DIHEDRAL ANGLE WAS RESTRAINED TO -60 REMARK 3 DEGREES PLUS-MINUS 30 DEGREES IF JHNHA < 5.5 HZ OR TO 110 DEGREES REMARK 3 PLUS-MINUS 50 DEGREES IF REMARK 3 JHNHA >8.0 HZ. CHI 1 DIHEDRAL ANGLES AND STEREOSPECIFIC REMARK 3 ASSIGNMENTS OF BETA- REMARK 3 METHYLENE PROTONS WERE DERIVED FROM JHNHB AND JHAHB SCALAR REMARK 3 COUPLING CONSTANTS REMARK 3 OBTAINED FROM 3D HNHB AND HACAHB-COSY EXPERIMENTS. TIGHT TURNS REMARK 3 CLEARLY REMARK 3 IDENTIFIED BY NOE PATTERNS AND J-COUPLING CONSTANTS, PHI AND PSI REMARK 3 ANGLES WERE REMARK 3 RESTRAINED TO THEIR STANDARD VALUES WITH PLUS-MINUS 30 DEGREES REMARK 3 ERROR RANGE. FOR RESIDUES HAVING INTENSE INTRARESIDUE HN-HA NOES REMARK 3 WITH POSITIVE PHI ANGLES SUGGESTED BY THE REMARK 3 PROGRAM TALOS, PHI WAS RESTRAINED TO 40 DEGREES PLUS-MINUS 15 REMARK 3 DEGREES. ELECTROSTATIC SURFACES WERE REMARK 3 CALCULATED USING GRASP. MOLECULAR MODELS WERE GENERATED WITH REMARK 3 QUANTA (MSI), REMARK 3 INSIGHT (MSI) AND MOLSCRIPT. REMARK 4 REMARK 4 1D8V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009899. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313.00 REMARK 210 PH : 5.50 REMARK 210 IONIC STRENGTH : 10 MM NAPI REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : ~0.7 MM PROTEIN MAP30 (15N/13C) REMARK 210 ENRICHED. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; REMARK 210 4D_13C/15N-SEPARATED_ NOESY; 3D_ REMARK 210 13C-SEPARATED_ NOESY; 4D_13C- REMARK 210 SEPARATED_ NOESY; HNHA; HNCA-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MODIFIED X-PLOR 3.5 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 THIS STRUCTURE WAS DETERMINED USING DIPOLAR COUPLING MEASURED IN REMARK 210 LIQUID REMARK 210 CRYSTAL MEDIA. IN ADDITION, WE ALSO MEASURED HYDROGEN BONDS REMARK 210 DIRECTLY AND USED REMARK 210 THEM IN STRUCTURE CALCULATIONS. 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 OG1 THR A 10 HG1 THR A 13 1.27 REMARK 500 O THR A 106 H ASN A 108 1.37 REMARK 500 O SER A 42 H ARG A 46 1.57 REMARK 500 O ASN A 141 H ALA A 145 1.58 REMARK 500 O THR A 10 H TYR A 14 1.60 REMARK 500 O LEU A 256 N GLY A 258 2.08 REMARK 500 O LEU A 152 OG1 THR A 156 2.18 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 PRO A 26 -169.22 -58.93 REMARK 500 PRO A 35 170.89 -59.27 REMARK 500 TYR A 38 -167.10 -65.86 REMARK 500 THR A 67 -85.35 -59.24 REMARK 500 ARG A 77 -123.60 46.26 REMARK 500 PHE A 83 -159.14 -86.71 REMARK 500 GLU A 85 -7.09 73.64 REMARK 500 SER A 86 -57.99 -163.22 REMARK 500 GLU A 89 -13.73 -47.30 REMARK 500 LEU A 94 -118.55 -49.77 REMARK 500 PRO A 104 -2.45 -58.20 REMARK 500 TYR A 139 49.26 -101.07 REMARK 500 TYR A 140 103.60 -29.54 REMARK 500 ALA A 145 -61.23 -29.96 REMARK 500 THR A 156 -60.40 -105.00 REMARK 500 ALA A 174 -40.92 -154.52 REMARK 500 PRO A 179 -148.68 -60.52 REMARK 500 LYS A 232 -155.93 -61.63 REMARK 500 LYS A 236 -89.02 -106.80 REMARK 500 ALA A 243 6.91 -170.53 REMARK 500 PHE A 250 -65.78 -129.73 REMARK 500 THR A 253 -13.98 70.57 REMARK 500 LEU A 256 109.16 11.05 REMARK 500 LEU A 257 -14.80 -33.04 REMARK 500 GLU A 259 166.02 -45.71 REMARK 500 VAL A 262 -89.96 -20.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 22 0.31 SIDE CHAIN REMARK 500 ARG A 45 0.15 SIDE CHAIN REMARK 500 ARG A 75 0.19 SIDE CHAIN REMARK 500 ARG A 77 0.14 SIDE CHAIN REMARK 500 ARG A 99 0.30 SIDE CHAIN REMARK 500 ARG A 120 0.30 SIDE CHAIN REMARK 500 ARG A 161 0.32 SIDE CHAIN REMARK 500 ARG A 208 0.22 SIDE CHAIN REMARK 500 ARG A 220 0.30 SIDE CHAIN REMARK 500 ARG A 242 0.32 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1D8V A 1 263 UNP P24817 RIP3_MOMCH 24 286 SEQADV 1D8V TYR A 14 UNP P24817 THR 37 CONFLICT SEQRES 1 A 263 ASP VAL ASN PHE ASP LEU SER THR ALA THR ALA LYS THR SEQRES 2 A 263 TYR THR LYS PHE ILE GLU ASP PHE ARG ALA THR LEU PRO SEQRES 3 A 263 PHE SER HIS LYS VAL TYR ASP ILE PRO LEU LEU TYR SER SEQRES 4 A 263 THR ILE SER ASP SER ARG ARG PHE ILE LEU LEU ASN LEU SEQRES 5 A 263 THR SER TYR ALA TYR GLU THR ILE SER VAL ALA ILE ASP SEQRES 6 A 263 VAL THR ASN VAL TYR VAL VAL ALA TYR ARG THR ARG ASP SEQRES 7 A 263 VAL SER TYR PHE PHE LYS GLU SER PRO PRO GLU ALA TYR SEQRES 8 A 263 ASN ILE LEU PHE LYS GLY THR ARG LYS ILE THR LEU PRO SEQRES 9 A 263 TYR THR GLY ASN TYR GLU ASN LEU GLN THR ALA ALA HIS SEQRES 10 A 263 LYS ILE ARG GLU ASN ILE ASP LEU GLY LEU PRO ALA LEU SEQRES 11 A 263 SER SER ALA ILE THR THR LEU PHE TYR TYR ASN ALA GLN SEQRES 12 A 263 SER ALA PRO SER ALA LEU LEU VAL LEU ILE GLN THR THR SEQRES 13 A 263 ALA GLU ALA ALA ARG PHE LYS TYR ILE GLU ARG HIS VAL SEQRES 14 A 263 ALA LYS TYR VAL ALA THR ASN PHE LYS PRO ASN LEU ALA SEQRES 15 A 263 ILE ILE SER LEU GLU ASN GLN TRP SER ALA LEU SER LYS SEQRES 16 A 263 GLN ILE PHE LEU ALA GLN ASN GLN GLY GLY LYS PHE ARG SEQRES 17 A 263 ASN PRO VAL ASP LEU ILE LYS PRO THR GLY GLU ARG PHE SEQRES 18 A 263 GLN VAL THR ASN VAL ASP SER ASP VAL VAL LYS GLY ASN SEQRES 19 A 263 ILE LYS LEU LEU LEU ASN SER ARG ALA SER THR ALA ASP SEQRES 20 A 263 GLU ASN PHE ILE THR THR MET THR LEU LEU GLY GLU SER SEQRES 21 A 263 VAL VAL ASN HELIX 1 1 THR A 10 LEU A 25 1 16 HELIX 2 2 SER A 42 ARG A 46 1 5 HELIX 3 3 PRO A 88 LEU A 94 1 7 HELIX 4 4 ASN A 108 HIS A 117 1 10 HELIX 5 5 ILE A 119 ILE A 123 5 5 HELIX 6 6 GLY A 126 TYR A 139 1 14 HELIX 7 7 GLN A 143 THR A 156 1 14 HELIX 8 8 THR A 156 PHE A 162 1 7 HELIX 9 9 PHE A 162 TYR A 172 1 11 HELIX 10 10 ASN A 180 GLY A 204 1 25 HELIX 11 11 ALA A 243 ASN A 249 5 7 SHEET 1 A 6 VAL A 2 ASP A 5 0 SHEET 2 A 6 PHE A 47 THR A 53 1 O LEU A 49 N VAL A 2 SHEET 3 A 6 THR A 59 ASP A 65 -1 N ILE A 60 O LEU A 52 SHEET 4 A 6 VAL A 71 THR A 76 -1 N VAL A 72 O ALA A 63 SHEET 5 A 6 VAL A 79 LYS A 84 -1 N VAL A 79 O THR A 76 SHEET 6 A 6 ARG A 99 THR A 106 1 O ARG A 99 N SER A 80 SHEET 1 B 2 LEU A 36 LEU A 37 0 SHEET 2 B 2 LEU A 238 LEU A 239 1 O LEU A 238 N LEU A 37 SHEET 1 C 2 LYS A 206 LYS A 215 0 SHEET 2 C 2 GLU A 219 ASN A 225 -1 O GLU A 219 N LYS A 215 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