HEADER STRUCTURAL PROTEIN 03-FEB-22 7TV2 TITLE X-RAY CRYSTAL STRUCTURE OF HIV-2 CA PROTEIN CTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MATRIX PROTEIN P17,NUCLEOCAPSID PROTEIN P7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE SOURCE 3 ROD); SOURCE 4 ORGANISM_TAXID: 11720; SOURCE 5 GENE: GAG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.SHI,H.AIHARA REVDAT 3 25-OCT-23 7TV2 1 SOURCE REVDAT 2 14-JUN-23 7TV2 1 JRNL REVDAT 1 17-MAY-23 7TV2 0 JRNL AUTH N.TALLEDGE,H.YANG,K.SHI,R.CORAY,G.YU,W.G.ARNDT,S.MENG, JRNL AUTH 2 G.C.BAXTER,L.M.MENDONCA,D.CASTANO-DIEZ,H.AIHARA,L.M.MANSKY, JRNL AUTH 3 W.ZHANG JRNL TITL HIV-2 IMMATURE PARTICLE MORPHOLOGY PROVIDES INSIGHTS INTO JRNL TITL 2 GAG LATTICE STABILITY AND VIRUS MATURATION. JRNL REF J.MOL.BIOL. V. 435 68143 2023 JRNL REFN ESSN 1089-8638 JRNL PMID 37150290 JRNL DOI 10.1016/J.JMB.2023.168143 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 4750 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) : 0.204 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 237 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 24.4100 - 4.2600 0.92 467 11 0.1642 0.2150 REMARK 3 2 4.2500 - 3.3800 0.91 438 23 0.1816 0.1955 REMARK 3 3 3.3800 - 2.9600 0.97 440 42 0.2056 0.2365 REMARK 3 4 2.9600 - 2.6900 0.96 445 29 0.2273 0.2787 REMARK 3 5 2.6900 - 2.4900 0.97 452 25 0.2201 0.3161 REMARK 3 6 2.4900 - 2.3500 0.97 464 20 0.2422 0.3650 REMARK 3 7 2.3500 - 2.2300 0.98 446 17 0.2501 0.2192 REMARK 3 8 2.2300 - 2.1300 0.96 461 18 0.2702 0.2740 REMARK 3 9 2.1300 - 2.0500 0.97 442 25 0.2566 0.3060 REMARK 3 10 2.0500 - 1.9800 0.96 458 27 0.3073 0.3189 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.20 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 : 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 : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 282 THROUGH 294 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7227 -6.3503 41.1235 REMARK 3 T TENSOR REMARK 3 T11: 0.3306 T22: 0.4148 REMARK 3 T33: 0.3679 T12: -0.0151 REMARK 3 T13: 0.0509 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 5.5945 L22: 7.6362 REMARK 3 L33: 7.7144 L12: 5.5753 REMARK 3 L13: -5.9022 L23: -6.9648 REMARK 3 S TENSOR REMARK 3 S11: 0.6249 S12: -0.9919 S13: 0.7327 REMARK 3 S21: 0.7189 S22: -0.4736 S23: 0.2575 REMARK 3 S31: -1.3839 S32: 0.3916 S33: -0.1224 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 295 THROUGH 309 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9173 -13.9080 39.7549 REMARK 3 T TENSOR REMARK 3 T11: 0.3213 T22: 0.4265 REMARK 3 T33: 0.2564 T12: 0.0310 REMARK 3 T13: 0.0493 T23: -0.0533 REMARK 3 L TENSOR REMARK 3 L11: 5.9727 L22: 3.9609 REMARK 3 L33: 6.1541 L12: -2.2488 REMARK 3 L13: 3.3260 L23: -4.8890 REMARK 3 S TENSOR REMARK 3 S11: -0.2645 S12: -0.3561 S13: -0.0893 REMARK 3 S21: 0.4748 S22: -0.0858 S23: -0.2483 REMARK 3 S31: -0.0124 S32: 0.3635 S33: 0.3171 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 310 THROUGH 321 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.5929 -22.2013 43.2963 REMARK 3 T TENSOR REMARK 3 T11: 0.4299 T22: 0.5607 REMARK 3 T33: 0.6737 T12: -0.0466 REMARK 3 T13: 0.1765 T23: -0.0207 REMARK 3 L TENSOR REMARK 3 L11: 3.6117 L22: 9.0175 REMARK 3 L33: 3.5796 L12: 3.5114 REMARK 3 L13: -3.3545 L23: -3.1199 REMARK 3 S TENSOR REMARK 3 S11: -1.0781 S12: 0.1964 S13: -1.9720 REMARK 3 S21: -0.5901 S22: -0.0616 S23: -1.0129 REMARK 3 S31: 0.7981 S32: -0.6905 S33: 1.1035 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 322 THROUGH 344 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1532 -11.7218 32.7037 REMARK 3 T TENSOR REMARK 3 T11: 0.2755 T22: 0.8107 REMARK 3 T33: 0.4025 T12: -0.0253 REMARK 3 T13: 0.0422 T23: 0.2173 REMARK 3 L TENSOR REMARK 3 L11: 5.9858 L22: 0.5832 REMARK 3 L33: 6.0940 L12: -1.2012 REMARK 3 L13: -0.8109 L23: -0.0935 REMARK 3 S TENSOR REMARK 3 S11: 0.0762 S12: 0.7424 S13: 0.3156 REMARK 3 S21: -0.1411 S22: 0.4276 S23: 0.2990 REMARK 3 S31: 0.0253 S32: -1.3410 S33: -0.4354 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 345 THROUGH 365 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7168 -8.8758 22.4615 REMARK 3 T TENSOR REMARK 3 T11: 0.3833 T22: 0.7471 REMARK 3 T33: 0.3367 T12: -0.1344 REMARK 3 T13: 0.0554 T23: 0.0582 REMARK 3 L TENSOR REMARK 3 L11: 2.7446 L22: 7.3891 REMARK 3 L33: 3.5904 L12: -1.1877 REMARK 3 L13: 0.6378 L23: -4.4704 REMARK 3 S TENSOR REMARK 3 S11: -0.0481 S12: 0.8723 S13: 0.3625 REMARK 3 S21: -0.7349 S22: 0.5333 S23: -0.2071 REMARK 3 S31: 0.6315 S32: -0.2274 S33: -0.2765 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 7TV2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000262957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4761 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 26.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.25700 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: PHASER REMARK 200 STARTING MODEL: 6AXX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M TRI-SODIUM CITRATE, 0.1M BIS REMARK 280 -TRIS PROPANE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 24.40650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.45950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.40650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.45950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -0.45442 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.49178 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 GLY A 278 REMARK 465 PRO A 279 REMARK 465 ASN A 280 REMARK 465 PRO A 281 DBREF1 7TV2 A 280 365 UNP A0A7D6CKX3_9HIV2 DBREF2 7TV2 A A0A7D6CKX3 280 365 SEQADV 7TV2 GLY A 278 UNP A0A7D6CKX EXPRESSION TAG SEQADV 7TV2 PRO A 279 UNP A0A7D6CKX EXPRESSION TAG SEQRES 1 A 88 GLY PRO ASN PRO THR ASN ILE LEU ASP ILE LYS GLN GLY SEQRES 2 A 88 PRO LYS GLU PRO PHE GLN SER TYR VAL ASP ARG PHE TYR SEQRES 3 A 88 LYS SER LEU ARG ALA GLU GLN THR ASP PRO ALA VAL LYS SEQRES 4 A 88 ASN TRP MET THR GLN THR LEU LEU VAL GLN ASN ALA ASN SEQRES 5 A 88 PRO ASP CYS LYS LEU VAL LEU LYS GLY LEU GLY MET ASN SEQRES 6 A 88 PRO THR LEU GLU GLU MET LEU THR ALA CYS GLN GLY VAL SEQRES 7 A 88 GLY GLY PRO GLY GLN LYS ALA ARG LEU MET FORMUL 2 HOH *25(H2 O) HELIX 1 AA1 THR A 282 ILE A 287 5 6 HELIX 2 AA2 PRO A 294 GLN A 310 1 17 HELIX 3 AA3 ASP A 312 THR A 322 1 11 HELIX 4 AA4 THR A 322 ASN A 327 1 6 HELIX 5 AA5 ASN A 329 GLY A 338 1 10 HELIX 6 AA6 THR A 344 GLN A 353 1 10 HELIX 7 AA7 GLY A 357 MET A 365 5 9 CRYST1 48.813 30.919 46.494 90.00 90.56 90.00 C 1 2 1 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 0.020486 0.000000 0.000200 0.00000 SCALE2 0.000000 0.032343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021509 0.00000