HEADER VIRAL PROTEIN 04-JUN-19 6K6M TITLE CRYSTAL STRUCTURE OF HIV-2 NEF PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NEF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_TAXID: 12721; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACCESSORY PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.HIRAO,S.ANDREWS,K.KUROKI,H.KUSAKA,T.TADOKORO,S.KITA,T.OSE, AUTHOR 2 S.ROWLAND-JONES,K.MAENAKA REVDAT 3 22-NOV-23 6K6M 1 REMARK REVDAT 2 21-APR-21 6K6M 1 JRNL REVDAT 1 25-MAR-20 6K6M 0 JRNL AUTH K.HIRAO,S.ANDREWS,K.KUROKI,H.KUSAKA,T.TADOKORO,S.KITA,T.OSE, JRNL AUTH 2 S.L.ROWLAND-JONES,K.MAENAKA JRNL TITL STRUCTURE OF HIV-2 NEF REVEALS FEATURES DISTINCT FROM HIV-1 JRNL TITL 2 INVOLVED IN IMMUNE REGULATION. JRNL REF ISCIENCE V. 23 00758 2020 JRNL REFN ESSN 2589-0042 JRNL PMID 31927483 JRNL DOI 10.1016/J.ISCI.2019.100758 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12874 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 631 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 40.1778 - 3.5424 1.00 2588 126 0.1931 0.2179 REMARK 3 2 3.5424 - 2.8119 1.00 2453 119 0.2067 0.2276 REMARK 3 3 2.8119 - 2.4565 1.00 2435 113 0.2166 0.2615 REMARK 3 4 2.4565 - 2.2320 1.00 2390 134 0.2198 0.3052 REMARK 3 5 2.2320 - 2.0720 1.00 2377 139 0.2342 0.2808 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.002 1243 REMARK 3 ANGLE : 0.555 1683 REMARK 3 CHIRALITY : 0.042 164 REMARK 3 PLANARITY : 0.005 217 REMARK 3 DIHEDRAL : 17.556 471 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 6K6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12922 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 44.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.77900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: 1AVV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 10% PEG 3350, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 21.78850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.81800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.81800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.78850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.38500 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 HIS A 88 REMARK 465 MET A 89 REMARK 465 VAL A 90 REMARK 465 ASP A 91 REMARK 465 SER A 92 REMARK 465 ASP A 93 REMARK 465 ASP A 94 REMARK 465 ASP A 95 REMARK 465 ASP A 96 REMARK 465 LEU A 97 REMARK 465 VAL A 98 REMARK 465 GLY A 99 REMARK 465 VAL A 100 REMARK 465 PRO A 101 REMARK 465 VAL A 102 REMARK 465 SER A 103 REMARK 465 HIS A 182 REMARK 465 PRO A 183 REMARK 465 GLN A 184 REMARK 465 GLU A 185 REMARK 465 GLN A 199 REMARK 465 VAL A 200 REMARK 465 SER A 201 REMARK 465 LYS A 202 REMARK 465 HIS A 203 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 LEU A 129 -43.63 69.56 REMARK 500 LEU A 174 32.37 -97.74 REMARK 500 ASN A 188 74.44 -107.51 REMARK 500 HIS A 196 75.99 -153.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 6K6M A 88 256 PDB 6K6M 6K6M 88 256 SEQRES 1 A 169 HIS MET VAL ASP SER ASP ASP ASP ASP LEU VAL GLY VAL SEQRES 2 A 169 PRO VAL SER PRO LYS VAL PRO LEU ARG THR MET THR PRO SEQRES 3 A 169 ARG LEU ALA ARG ASP MET SER PHE LEU ILE LYS ASP LYS SEQRES 4 A 169 GLY GLY LEU GLU GLY MET TYR TYR SER ARG ARG ARG HIS SEQRES 5 A 169 ARG ILE LEU ASP ILE TYR LEU GLU LYS GLU GLU GLY ILE SEQRES 6 A 169 ILE PRO ASP TRP HIS ASN TYR THR HIS GLY PRO GLY ILE SEQRES 7 A 169 ARG PHE PRO LYS CYS PRO GLY TRP LEU TRP LYS LEU VAL SEQRES 8 A 169 PRO VAL ASP HIS PRO GLN GLU GLU GLN ASN ASP GLU ALA SEQRES 9 A 169 ASN TYR LEU LEU HIS PRO ALA GLN VAL SER LYS HIS ASP SEQRES 10 A 169 ASP PRO HIS GLY GLU THR LEU VAL TRP ARG PHE ASP PRO SEQRES 11 A 169 MET LEU ALA HIS GLU TYR VAL ALA PHE LYS LYS TYR PRO SEQRES 12 A 169 GLU GLU PHE GLY TYR GLN SER GLY LEU PRO GLU ASP VAL SEQRES 13 A 169 TRP LYS ALA LYS LEU LYS ALA ARG GLY ILE PRO PHE ASN FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 THR A 112 LYS A 126 1 15 HELIX 2 AA2 SER A 135 GLY A 151 1 17 HELIX 3 AA3 ASN A 188 HIS A 196 1 9 HELIX 4 AA4 PRO A 217 HIS A 221 5 5 HELIX 5 AA5 TYR A 223 TYR A 229 1 7 HELIX 6 AA6 PRO A 230 SER A 237 5 8 HELIX 7 AA7 PRO A 240 ARG A 251 1 12 SHEET 1 AA1 2 TRP A 175 VAL A 180 0 SHEET 2 AA1 2 THR A 210 PHE A 215 -1 O THR A 210 N VAL A 180 CISPEP 1 GLY A 162 PRO A 163 0 3.30 CRYST1 43.577 44.770 103.636 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 0.022948 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009649 0.00000