HEADER APOPTOSIS 05-AUG-11 3TB8 TITLE CRYSTAL STRUCTURE OF FULL-LENGTH MYRISTOYLATED HIV-1 NEF CAVEAT 3TB8 THE COORDINATES CONTAIN ONLY THE CA ATOMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NEF; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3'ORF, NEGATIVE FACTOR, F-PROTEIN, C-TERMINAL CORE PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: MYRISTOYLATED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11678; SOURCE 5 STRAIN: BH10; SOURCE 6 GENE: NEF; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS F-PROTEIN (PF00469), APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR C.A.DENNIS,M.HARRIS,J.JAEGER REVDAT 3 22-MAY-24 3TB8 1 REMARK REVDAT 2 21-DEC-22 3TB8 1 SEQADV REVDAT 1 03-OCT-12 3TB8 0 JRNL AUTH C.A.DENNIS,M.HARRIS,J.JAEGER JRNL TITL CRYSTAL STRUCTURE OF FULL-LENGTH MYRISTOYLATED HIV-1 NEF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.2_432 - REFINE REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 2622 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.337 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.280 REMARK 3 FREE R VALUE TEST SET COUNT : 86 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 0.0000 - 3.7100 0.96 2436 86 0.2308 0.3366 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.00 REMARK 3 B_SOL : 0.19 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.36620 REMARK 3 B22 (A**2) : 11.22480 REMARK 3 B33 (A**2) : -3.85870 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3TB8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : YALE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2622 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.710 REMARK 200 RESOLUTION RANGE LOW (A) : 28.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX - PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% POLYETHYLENEGLYCOL 3350, LITHIUM REMARK 280 SULFATE, HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 44.66500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.89000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 13.89000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.66500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.66500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 204 REMARK 465 ASN A 205 REMARK 465 CYS A 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AVV RELATED DB: PDB REMARK 900 RELATED ID: 1EFN RELATED DB: PDB DBREF 3TB8 A 2 206 UNP P03404 NEF_HV1B1 2 206 SEQADV 3TB8 MYR A 1 UNP P03404 MODIFIED RESIDUE SEQRES 1 A 206 MYR GLY GLY LYS TRP SER LYS SER SER VAL ILE GLY TRP SEQRES 2 A 206 PRO ALA VAL ARG GLU ARG MET ARG ARG ALA GLU PRO ALA SEQRES 3 A 206 ALA ASP GLY VAL GLY ALA ALA SER ARG ASP LEU GLU LYS SEQRES 4 A 206 HIS GLY ALA ILE THR SER SER ASN THR ALA ALA ASN ASN SEQRES 5 A 206 ALA ALA CYS ALA TRP LEU GLU ALA GLN GLU GLU GLU LYS SEQRES 6 A 206 VAL GLY PHE PRO VAL THR PRO GLN VAL PRO LEU ARG PRO SEQRES 7 A 206 MET THR TYR LYS ALA ALA VAL ASP LEU SER HIS PHE LEU SEQRES 8 A 206 LYS GLU LYS GLY GLY LEU GLU GLY LEU ILE HIS SER GLN SEQRES 9 A 206 ARG ARG GLN ASP ILE LEU ASP LEU TRP ILE TYR HIS THR SEQRES 10 A 206 GLN GLY TYR PHE PRO ASP TRP GLN ASN TYR THR PRO GLY SEQRES 11 A 206 PRO GLY ILE ARG TYR PRO LEU THR PHE GLY TRP CYS TYR SEQRES 12 A 206 LYS LEU VAL PRO VAL GLU PRO ASP LYS VAL GLU GLU ALA SEQRES 13 A 206 ASN LYS GLY GLU ASN THR SER LEU LEU HIS PRO VAL SER SEQRES 14 A 206 LEU HIS GLY MET ASP ASP PRO GLU ARG GLU VAL LEU GLU SEQRES 15 A 206 TRP ARG PHE ASP SER ARG LEU ALA PHE HIS HIS VAL ALA SEQRES 16 A 206 ARG GLU LEU HIS PRO GLU TYR PHE LYS ASN CYS HET MYR A 1 1 HETNAM MYR MYRISTIC ACID FORMUL 1 MYR C14 H28 O2 CRYST1 89.330 89.330 27.780 90.00 90.00 90.00 P 21 21 21 4 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 0.011194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035997 0.00000 HETATM 1 C1 MYR A 1 13.144 0.663 25.060 1.00139.80 C