HEADER AIDS 07-MAY-98 1BDE TITLE HELICAL STRUCTURE OF POLYPEPTIDES FROM THE C-TERMINAL HALF OF HIV-1 TITLE 2 VPR, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: VPR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VPR 50-82; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RESIDUES 50 - 82 FROM HIV VPR KEYWDS AIDS, HIV, VIRAL PROTEIN, VPR FRAGMENT, HELIX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.YAO,A.A.AZAD,I.G.MACREADIE,R.S.NORTON REVDAT 5 16-OCT-24 1BDE 1 REMARK REVDAT 4 16-FEB-22 1BDE 1 REMARK LINK REVDAT 3 24-FEB-09 1BDE 1 VERSN REVDAT 2 13-JAN-99 1BDE 3 HET COMPND REMARK TITLE REVDAT 2 2 3 HETATM SEQADV HEADER TER REVDAT 2 3 3 LINK SOURCE SEQRES FORMUL REVDAT 2 4 3 JRNL KEYWDS HELIX CONECT REVDAT 1 02-DEC-98 1BDE 0 JRNL AUTH S.YAO,A.M.TORRES,A.A.AZAD,I.G.MACREADIE,R.S.NORTON JRNL TITL SOLUTION STRUCTURE OF PEPTIDES FROM HIV-1 VPR PROTEIN THAT JRNL TITL 2 CAUSE MEMBRANE PERMEABILIZATION AND GROWTH ARREST. JRNL REF J.PEPT.SCI. V. 4 426 1998 JRNL REFN ISSN 1075-2617 JRNL PMID 9851370 JRNL DOI 10.1002/(SICI)1099-1387(199811)4:7<426::AID-PSC161>3.0.CO;2- JRNL DOI 2 J REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL STRUCTURE CALCULATION WAS REMARK 3 PERFORMED USING DYANA 1.4. THE BEST 100 STRUCTURES WERE FURTHER REMARK 3 REFINED IN X-PLOR 3.8. REMARK 4 REMARK 4 1BDE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171620. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 50% TFE-D3/50% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TOCSY; NOESY; DQFCOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.8 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D 1H NMR SPECTROSCOPY. 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: 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 1 HIS A 71 NE2 HIS A 71 CD2 -0.066 REMARK 500 1 HIS A 78 NE2 HIS A 78 CD2 -0.067 REMARK 500 2 HIS A 78 NE2 HIS A 78 CD2 -0.067 REMARK 500 3 HIS A 71 NE2 HIS A 71 CD2 -0.067 REMARK 500 3 HIS A 78 NE2 HIS A 78 CD2 -0.067 REMARK 500 4 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 4 HIS A 78 NE2 HIS A 78 CD2 -0.066 REMARK 500 5 HIS A 71 NE2 HIS A 71 CD2 -0.066 REMARK 500 6 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 6 HIS A 78 NE2 HIS A 78 CD2 -0.067 REMARK 500 7 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 7 HIS A 78 NE2 HIS A 78 CD2 -0.066 REMARK 500 8 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 9 HIS A 71 NE2 HIS A 71 CD2 -0.067 REMARK 500 9 HIS A 78 NE2 HIS A 78 CD2 -0.066 REMARK 500 10 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 10 HIS A 78 NE2 HIS A 78 CD2 -0.068 REMARK 500 11 HIS A 71 NE2 HIS A 71 CD2 -0.067 REMARK 500 12 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 13 HIS A 71 NE2 HIS A 71 CD2 -0.069 REMARK 500 13 HIS A 78 NE2 HIS A 78 CD2 -0.068 REMARK 500 14 HIS A 71 NE2 HIS A 71 CD2 -0.066 REMARK 500 14 HIS A 78 NE2 HIS A 78 CD2 -0.066 REMARK 500 15 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 15 HIS A 78 NE2 HIS A 78 CD2 -0.067 REMARK 500 16 HIS A 71 NE2 HIS A 71 CD2 -0.067 REMARK 500 17 HIS A 78 NE2 HIS A 78 CD2 -0.068 REMARK 500 18 HIS A 71 NE2 HIS A 71 CD2 -0.067 REMARK 500 18 HIS A 78 NE2 HIS A 78 CD2 -0.066 REMARK 500 19 HIS A 71 NE2 HIS A 71 CD2 -0.067 REMARK 500 19 HIS A 78 NE2 HIS A 78 CD2 -0.067 REMARK 500 20 HIS A 71 NE2 HIS A 71 CD2 -0.068 REMARK 500 20 HIS A 78 NE2 HIS A 78 CD2 -0.067 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 ASP A 52 -46.36 -28.00 REMARK 500 1 CYS A 76 9.81 -59.84 REMARK 500 1 ARG A 80 39.30 -74.72 REMARK 500 2 ASP A 52 -54.48 -27.53 REMARK 500 2 ARG A 80 77.83 -118.79 REMARK 500 3 ASP A 52 -124.40 -90.28 REMARK 500 3 CYS A 76 4.84 -66.56 REMARK 500 3 SER A 79 -134.27 -122.29 REMARK 500 4 ASP A 52 -60.25 -29.29 REMARK 500 4 ARG A 80 44.28 32.83 REMARK 500 4 ILE A 81 83.19 -66.62 REMARK 500 5 SER A 79 123.76 134.26 REMARK 500 5 ARG A 80 69.01 -177.57 REMARK 500 7 ASP A 52 -120.58 -135.54 REMARK 500 7 SER A 79 92.32 168.91 REMARK 500 8 ASP A 52 -114.84 -125.79 REMARK 500 8 THR A 53 -35.86 -33.49 REMARK 500 8 SER A 79 155.07 170.01 REMARK 500 8 ILE A 81 -123.48 42.36 REMARK 500 9 ASP A 52 -102.07 -132.97 REMARK 500 9 SER A 79 74.37 83.00 REMARK 500 9 ARG A 80 76.75 -110.31 REMARK 500 10 ASP A 52 -73.56 -88.83 REMARK 500 10 ILE A 74 -64.84 -94.39 REMARK 500 10 SER A 79 105.22 78.51 REMARK 500 11 ASP A 52 -58.04 -27.04 REMARK 500 11 ILE A 74 -70.78 -84.59 REMARK 500 11 SER A 79 117.62 -162.59 REMARK 500 11 ARG A 80 -66.45 -159.81 REMARK 500 12 SER A 79 -46.15 164.76 REMARK 500 13 ASP A 52 -119.40 -125.55 REMARK 500 13 SER A 79 40.77 -171.67 REMARK 500 13 ARG A 80 68.62 31.50 REMARK 500 14 ILE A 74 -61.93 -95.20 REMARK 500 14 HIS A 78 -73.02 -53.21 REMARK 500 14 SER A 79 -165.47 153.35 REMARK 500 15 ASP A 52 -123.40 -102.05 REMARK 500 15 SER A 79 -1.02 161.43 REMARK 500 16 SER A 79 119.63 174.63 REMARK 500 16 ARG A 80 95.94 -161.62 REMARK 500 17 ASP A 52 -100.29 -108.66 REMARK 500 17 ARG A 80 57.67 -115.88 REMARK 500 18 ASP A 52 -73.46 -114.55 REMARK 500 18 SER A 79 14.25 54.60 REMARK 500 18 ILE A 81 74.71 -62.16 REMARK 500 19 ASP A 52 -62.78 69.35 REMARK 500 19 TRP A 54 -71.91 -44.01 REMARK 500 19 SER A 79 63.15 176.82 REMARK 500 19 ARG A 80 25.40 42.70 REMARK 500 20 ASP A 52 -120.51 -118.26 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. 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 1 ARG A 62 0.20 SIDE CHAIN REMARK 500 1 ARG A 73 0.24 SIDE CHAIN REMARK 500 1 ARG A 77 0.32 SIDE CHAIN REMARK 500 1 ARG A 80 0.27 SIDE CHAIN REMARK 500 2 ARG A 62 0.31 SIDE CHAIN REMARK 500 2 ARG A 73 0.31 SIDE CHAIN REMARK 500 2 ARG A 77 0.30 SIDE CHAIN REMARK 500 2 ARG A 80 0.30 SIDE CHAIN REMARK 500 3 ARG A 62 0.32 SIDE CHAIN REMARK 500 3 ARG A 73 0.28 SIDE CHAIN REMARK 500 3 ARG A 77 0.32 SIDE CHAIN REMARK 500 3 ARG A 80 0.27 SIDE CHAIN REMARK 500 4 ARG A 62 0.32 SIDE CHAIN REMARK 500 4 ARG A 73 0.32 SIDE CHAIN REMARK 500 4 ARG A 77 0.29 SIDE CHAIN REMARK 500 4 ARG A 80 0.30 SIDE CHAIN REMARK 500 5 ARG A 62 0.31 SIDE CHAIN REMARK 500 5 ARG A 73 0.12 SIDE CHAIN REMARK 500 5 ARG A 77 0.26 SIDE CHAIN REMARK 500 5 ARG A 80 0.29 SIDE CHAIN REMARK 500 6 ARG A 62 0.30 SIDE CHAIN REMARK 500 6 ARG A 73 0.31 SIDE CHAIN REMARK 500 6 ARG A 77 0.28 SIDE CHAIN REMARK 500 6 ARG A 80 0.17 SIDE CHAIN REMARK 500 7 ARG A 62 0.32 SIDE CHAIN REMARK 500 7 ARG A 73 0.30 SIDE CHAIN REMARK 500 7 ARG A 77 0.32 SIDE CHAIN REMARK 500 7 ARG A 80 0.23 SIDE CHAIN REMARK 500 8 ARG A 62 0.22 SIDE CHAIN REMARK 500 8 ARG A 73 0.29 SIDE CHAIN REMARK 500 8 ARG A 77 0.29 SIDE CHAIN REMARK 500 8 ARG A 80 0.28 SIDE CHAIN REMARK 500 9 ARG A 62 0.21 SIDE CHAIN REMARK 500 9 ARG A 73 0.29 SIDE CHAIN REMARK 500 9 ARG A 77 0.27 SIDE CHAIN REMARK 500 9 ARG A 80 0.29 SIDE CHAIN REMARK 500 10 ARG A 62 0.20 SIDE CHAIN REMARK 500 10 ARG A 73 0.21 SIDE CHAIN REMARK 500 10 ARG A 77 0.23 SIDE CHAIN REMARK 500 10 ARG A 80 0.31 SIDE CHAIN REMARK 500 11 ARG A 62 0.25 SIDE CHAIN REMARK 500 11 ARG A 73 0.31 SIDE CHAIN REMARK 500 11 ARG A 77 0.31 SIDE CHAIN REMARK 500 11 ARG A 80 0.31 SIDE CHAIN REMARK 500 12 ARG A 62 0.30 SIDE CHAIN REMARK 500 12 ARG A 73 0.31 SIDE CHAIN REMARK 500 12 ARG A 77 0.25 SIDE CHAIN REMARK 500 12 ARG A 80 0.31 SIDE CHAIN REMARK 500 13 ARG A 62 0.27 SIDE CHAIN REMARK 500 13 ARG A 73 0.31 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 79 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1BDE A 50 82 UNP P12520 VPR_HV1N5 50 82 SEQRES 1 A 35 ACE TYR GLY ASP THR TRP ALA GLY VAL GLU ALA ILE ILE SEQRES 2 A 35 ARG ILE LEU GLN GLN LEU LEU PHE ILE HIS PHE ARG ILE SEQRES 3 A 35 GLY CYS ARG HIS SER ARG ILE GLY NH2 HET ACE A 50A 6 HET NH2 A 83 3 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N HELIX 1 H1 THR A 53 HIS A 78 1 26 LINK C ACE A 50A N TYR A 50 1555 1555 1.31 LINK C GLY A 82 N NH2 A 83 1555 1555 1.30 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 HETATM 1 C ACE A 50A 1.847 -0.476 1.022 1.00 1.00 C HETATM 2 O ACE A 50A 0.813 -0.704 1.614 1.00 1.00 O HETATM 3 CH3 ACE A 50A 3.052 0.082 1.770 1.00 1.00 C HETATM 4 H1 ACE A 50A 3.633 0.714 1.114 1.00 1.00 H HETATM 5 H2 ACE A 50A 3.657 -0.735 2.133 1.00 1.00 H HETATM 6 H3 ACE A 50A 2.695 0.664 2.608 1.00 1.00 H