PDB Short entry for 1VPU HEADER AIDS 28-JAN-97 1VPU TITLE NMR SOLUTION STRUCTURE OF THE HIV-1 VPU CYTOPLASMIC DOMAIN, 9 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: VPU PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYTOPLASMIC DOMAIN RESIDUES 39 - 81; COMPND 5 SYNONYM: VPU(39-81); COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: SF162 ISOLATE; SOURCE 5 CELL_LINE: BL21; SOURCE 6 GENE: SYNTHETIC GENE; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PET16B (NOVAGEN); SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET16B (NOVAGEN) KEYWDS HIV, VPU, AIDS EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR D.WILLBOLD,S.HOFFMANN,P.ROSCH REVDAT 3 02-MAR-22 1VPU 1 REMARK REVDAT 2 24-FEB-09 1VPU 1 VERSN REVDAT 1 15-MAY-97 1VPU 0 JRNL AUTH D.WILLBOLD,S.HOFFMANN,P.ROSCH JRNL TITL SECONDARY STRUCTURE AND TERTIARY FOLD OF THE HUMAN JRNL TITL 2 IMMUNODEFICIENCY VIRUS PROTEIN U (VPU) CYTOPLASMIC DOMAIN IN JRNL TITL 3 SOLUTION. JRNL REF EUR.J.BIOCHEM. V. 245 581 1997 JRNL REFN ISSN 0014-2956 JRNL PMID 9182993 JRNL DOI 10.1111/J.1432-1033.1997.T01-1-00581.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VPU 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_1000177092. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY (100; 150; 200 MS MIXING REMARK 210 TIME) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY, AGREEMENT WITH REMARK 210 EXPERIMENTAL DATA REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: REPRESENTATIVE MODEL NUMBER: 3 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: 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 ILE A 39 -77.64 -64.25 REMARK 500 1 GLU A 51 6.65 56.64 REMARK 500 1 GLU A 56 98.13 -69.49 REMARK 500 1 SER A 57 -11.62 78.10 REMARK 500 1 GLU A 58 -129.00 37.06 REMARK 500 1 LEU A 64 -85.58 -96.63 REMARK 500 1 SER A 65 160.81 59.91 REMARK 500 1 ALA A 66 -64.32 65.00 REMARK 500 1 ARG A 70 104.76 -46.00 REMARK 500 1 LEU A 73 105.96 -51.01 REMARK 500 1 ALA A 74 -170.94 -172.08 REMARK 500 2 ASP A 40 -25.73 74.97 REMARK 500 2 GLU A 51 -30.87 61.79 REMARK 500 2 SER A 53 33.67 -93.07 REMARK 500 2 GLU A 58 -62.68 71.51 REMARK 500 2 SER A 65 -90.96 60.00 REMARK 500 2 GLU A 69 42.75 -84.12 REMARK 500 2 HIS A 72 -46.23 177.48 REMARK 500 2 LEU A 73 90.71 20.56 REMARK 500 2 ALA A 74 -165.67 -176.38 REMARK 500 3 GLU A 51 14.59 54.18 REMARK 500 3 SER A 57 47.83 -164.52 REMARK 500 3 LEU A 67 -60.14 -107.52 REMARK 500 3 VAL A 68 72.14 47.90 REMARK 500 3 ARG A 70 79.91 -67.10 REMARK 500 3 HIS A 72 94.32 41.51 REMARK 500 3 ALA A 74 -170.63 -170.56 REMARK 500 4 GLN A 38 84.11 -172.49 REMARK 500 4 ILE A 39 -109.90 -81.20 REMARK 500 4 GLU A 51 13.49 54.81 REMARK 500 4 GLU A 58 -109.83 50.98 REMARK 500 4 GLU A 69 -9.14 -59.91 REMARK 500 4 ARG A 70 108.59 -43.88 REMARK 500 4 ALA A 74 -171.34 -171.77 REMARK 500 5 GLN A 38 58.58 -141.78 REMARK 500 5 GLU A 51 -43.86 57.32 REMARK 500 5 SER A 53 39.10 -98.99 REMARK 500 5 GLU A 58 75.52 57.35 REMARK 500 5 LEU A 64 -42.04 -174.81 REMARK 500 5 SER A 65 -44.98 -21.27 REMARK 500 5 ALA A 66 -66.60 -16.02 REMARK 500 5 LEU A 67 -79.87 -99.25 REMARK 500 5 ALA A 74 -160.04 -160.55 REMARK 500 5 PRO A 75 -93.70 -62.77 REMARK 500 5 TRP A 76 -80.64 26.32 REMARK 500 6 GLU A 51 10.05 56.72 REMARK 500 6 SER A 57 -62.89 72.85 REMARK 500 6 GLU A 58 124.19 75.25 REMARK 500 6 SER A 65 -58.42 64.97 REMARK 500 6 VAL A 68 58.85 -91.56 REMARK 500 REMARK 500 THIS ENTRY HAS 83 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 41 0.32 SIDE CHAIN REMARK 500 1 ARG A 45 0.29 SIDE CHAIN REMARK 500 1 ARG A 49 0.28 SIDE CHAIN REMARK 500 1 ARG A 70 0.29 SIDE CHAIN REMARK 500 2 ARG A 41 0.31 SIDE CHAIN REMARK 500 2 ARG A 45 0.28 SIDE CHAIN REMARK 500 2 ARG A 49 0.32 SIDE CHAIN REMARK 500 2 ARG A 70 0.28 SIDE CHAIN REMARK 500 3 ARG A 41 0.30 SIDE CHAIN REMARK 500 3 ARG A 45 0.32 SIDE CHAIN REMARK 500 3 ARG A 49 0.30 SIDE CHAIN REMARK 500 3 ARG A 70 0.32 SIDE CHAIN REMARK 500 4 ARG A 45 0.30 SIDE CHAIN REMARK 500 4 ARG A 49 0.25 SIDE CHAIN REMARK 500 4 ARG A 70 0.30 SIDE CHAIN REMARK 500 5 ARG A 41 0.28 SIDE CHAIN REMARK 500 5 ARG A 45 0.27 SIDE CHAIN REMARK 500 5 ARG A 49 0.29 SIDE CHAIN REMARK 500 5 ARG A 70 0.30 SIDE CHAIN REMARK 500 6 ARG A 41 0.26 SIDE CHAIN REMARK 500 6 ARG A 45 0.31 SIDE CHAIN REMARK 500 6 ARG A 49 0.32 SIDE CHAIN REMARK 500 6 ARG A 70 0.30 SIDE CHAIN REMARK 500 7 ARG A 41 0.27 SIDE CHAIN REMARK 500 7 ARG A 45 0.20 SIDE CHAIN REMARK 500 7 ARG A 49 0.26 SIDE CHAIN REMARK 500 7 ARG A 70 0.29 SIDE CHAIN REMARK 500 8 ARG A 41 0.31 SIDE CHAIN REMARK 500 8 ARG A 45 0.31 SIDE CHAIN REMARK 500 8 ARG A 49 0.29 SIDE CHAIN REMARK 500 8 ARG A 70 0.29 SIDE CHAIN REMARK 500 9 ARG A 41 0.31 SIDE CHAIN REMARK 500 9 ARG A 45 0.29 SIDE CHAIN REMARK 500 9 ARG A 49 0.26 SIDE CHAIN REMARK 500 9 ARG A 70 0.21 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1VPU A 39 81 UNP P19554 VPU_HV1S1 39 81 SEQRES 1 A 45 LEU GLN ILE ASP ARG LEU ILE ASP ARG ILE THR GLU ARG SEQRES 2 A 45 ALA GLU ASP SER GLY ASN GLU SER GLU GLY ASP GLN GLU SEQRES 3 A 45 GLU LEU SER ALA LEU VAL GLU ARG GLY HIS LEU ALA PRO SEQRES 4 A 45 TRP ASP VAL ASP ASP LEU HELIX 1 1 ASP A 40 ALA A 50 1 11 HELIX 2 2 ASP A 60 GLU A 63 5 4 HELIX 3 3 PRO A 75 VAL A 78 1 4 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