HEADER ONCOPROTEIN 11-MAY-23 8P14 TITLE USP28 USP DOMAIN IN COMPLEX WITH VISMODEGIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 28; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 28,UBIQUITIN THIOESTERASE 28, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 28; COMPND 6 EC: 3.4.19.12; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: UCID OLIGOMERIZATION DOMAIN REPLACED BY A LINKER,UCID COMPND 9 OLIGOMERIZATION DOMAIN REPLACED BY A LINKER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP28, KIAA1515; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, INHIBITOR, DEUBIQUITYLASE, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.SAUER,R.KARAL NAIR,C.KISKER REVDAT 1 22-MAY-24 8P14 0 JRNL AUTH F.SAUER,R.KARAL NAIR,C.KISKER JRNL TITL USP28 USP DOMAIN IN COMPLEX WITH VISMODEGIB JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44525 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1982 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 44.4600 - 6.1900 1.00 3050 137 0.1855 0.1815 REMARK 3 2 6.1900 - 4.9200 1.00 3043 148 0.1729 0.1909 REMARK 3 3 4.9100 - 4.2900 1.00 3030 146 0.1433 0.1616 REMARK 3 4 4.2900 - 3.9000 1.00 3040 139 0.1593 0.2286 REMARK 3 5 3.9000 - 3.6200 1.00 3040 141 0.1743 0.2434 REMARK 3 6 3.6200 - 3.4100 1.00 3045 135 0.1984 0.2268 REMARK 3 7 3.4100 - 3.2400 1.00 3031 142 0.1886 0.2061 REMARK 3 8 3.2400 - 3.1000 1.00 3060 140 0.2199 0.2383 REMARK 3 9 3.1000 - 2.9800 1.00 3025 145 0.2356 0.2398 REMARK 3 10 2.9800 - 2.8800 1.00 3046 139 0.2737 0.3471 REMARK 3 11 2.8800 - 2.7900 1.00 3031 143 0.3189 0.3728 REMARK 3 12 2.7900 - 2.7100 1.00 3069 145 0.3160 0.3327 REMARK 3 13 2.7100 - 2.6300 1.00 3024 140 0.3221 0.3328 REMARK 3 14 2.6300 - 2.5700 1.00 3009 142 0.3410 0.3602 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.940 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) : 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 : 0.005 2794 REMARK 3 ANGLE : 0.811 3799 REMARK 3 CHIRALITY : 0.051 387 REMARK 3 PLANARITY : 0.009 519 REMARK 3 DIHEDRAL : 13.302 1012 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 149 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.9194 4.8340 -38.0558 REMARK 3 T TENSOR REMARK 3 T11: 0.9397 T22: 0.6173 REMARK 3 T33: 0.7863 T12: 0.0625 REMARK 3 T13: -0.0510 T23: 0.2836 REMARK 3 L TENSOR REMARK 3 L11: 4.5344 L22: 6.6538 REMARK 3 L33: 3.2514 L12: -0.5318 REMARK 3 L13: -0.1306 L23: -0.0119 REMARK 3 S TENSOR REMARK 3 S11: 0.1376 S12: 0.4086 S13: 0.6062 REMARK 3 S21: -0.1375 S22: -0.0322 S23: -0.1517 REMARK 3 S31: -0.7798 S32: -0.1633 S33: -0.1369 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 228 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.0151 5.3066 -29.6756 REMARK 3 T TENSOR REMARK 3 T11: 1.1899 T22: 0.5573 REMARK 3 T33: 0.9886 T12: 0.0784 REMARK 3 T13: -0.2153 T23: 0.1334 REMARK 3 L TENSOR REMARK 3 L11: 3.3236 L22: 3.0872 REMARK 3 L33: 4.4668 L12: 1.1988 REMARK 3 L13: -1.6464 L23: 0.0600 REMARK 3 S TENSOR REMARK 3 S11: 0.1000 S12: -0.3333 S13: 0.9740 REMARK 3 S21: 0.5757 S22: -0.3220 S23: -0.2805 REMARK 3 S31: -0.6912 S32: 0.4415 S33: 0.2337 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 294 THROUGH 397 ) REMARK 3 ORIGIN FOR THE GROUP (A): 54.2834 -12.5623 -12.4086 REMARK 3 T TENSOR REMARK 3 T11: 0.7380 T22: 0.4934 REMARK 3 T33: 0.5217 T12: -0.0003 REMARK 3 T13: -0.1151 T23: -0.0816 REMARK 3 L TENSOR REMARK 3 L11: 1.9744 L22: 3.4358 REMARK 3 L33: 3.9349 L12: -0.9498 REMARK 3 L13: -1.6795 L23: 1.4930 REMARK 3 S TENSOR REMARK 3 S11: -0.0863 S12: -0.5592 S13: 0.3739 REMARK 3 S21: 0.7819 S22: 0.0652 S23: -0.4282 REMARK 3 S31: -0.1019 S32: 0.4325 S33: -0.0223 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 398 THROUGH 451 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.4043 -13.7782 -30.1814 REMARK 3 T TENSOR REMARK 3 T11: 0.5190 T22: 0.3092 REMARK 3 T33: 0.4128 T12: 0.0547 REMARK 3 T13: -0.1105 T23: 0.0299 REMARK 3 L TENSOR REMARK 3 L11: 4.9026 L22: 5.0095 REMARK 3 L33: 6.3178 L12: -0.1286 REMARK 3 L13: -1.5767 L23: 0.3732 REMARK 3 S TENSOR REMARK 3 S11: 0.0465 S12: 0.5291 S13: 0.3258 REMARK 3 S21: -0.0183 S22: -0.1621 S23: 0.1097 REMARK 3 S31: -0.3142 S32: -0.2348 S33: 0.1726 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 452 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.0021 -4.9814 -40.1900 REMARK 3 T TENSOR REMARK 3 T11: 0.7733 T22: 0.7524 REMARK 3 T33: 0.6102 T12: 0.0541 REMARK 3 T13: -0.0725 T23: 0.1745 REMARK 3 L TENSOR REMARK 3 L11: 1.3673 L22: 3.4572 REMARK 3 L33: 3.8940 L12: -0.0456 REMARK 3 L13: 0.0679 L23: -1.8148 REMARK 3 S TENSOR REMARK 3 S11: 0.0496 S12: 0.7255 S13: 0.6037 REMARK 3 S21: -0.3137 S22: 0.0109 S23: 0.3506 REMARK 3 S31: -0.6614 S32: -0.3051 S33: -0.0950 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 8P14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-21 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44538 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 REMARK 200 RESOLUTION RANGE LOW (A) : 47.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.68 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 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: 6H4I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M NACL 0.1 M LI2SO4 0.1 M MES PH REMARK 280 6.4 14% PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 53.31700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.78258 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 109.95233 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 53.31700 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.78258 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 109.95233 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 53.31700 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.78258 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 109.95233 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 53.31700 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 30.78258 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 109.95233 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 53.31700 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 30.78258 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 109.95233 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 53.31700 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 30.78258 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 109.95233 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 61.56517 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 219.90467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 61.56517 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 219.90467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 61.56517 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 219.90467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 61.56517 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 219.90467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 61.56517 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 219.90467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 61.56517 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 219.90467 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 148 REMARK 465 GLY A 244 REMARK 465 ALA A 245 REMARK 465 PHE A 246 REMARK 465 ARG A 247 REMARK 465 SER A 248 REMARK 465 SER A 249 REMARK 465 GLU A 250 REMARK 465 GLU A 251 REMARK 465 GLN A 252 REMARK 465 GLN A 253 REMARK 465 GLN A 254 REMARK 465 VAL A 277 REMARK 465 ASN A 278 REMARK 465 SER A 279 REMARK 465 PRO A 280 REMARK 465 ARG A 281 REMARK 465 ASN A 282 REMARK 465 LYS A 283 REMARK 465 GLY A 337 REMARK 465 ASP A 338 REMARK 465 VAL A 339 REMARK 465 GLU A 340 REMARK 465 LEU A 341 REMARK 465 LEU A 342 REMARK 465 PRO A 343 REMARK 465 SER A 344 REMARK 465 ASP A 345 REMARK 465 HIS A 346 REMARK 465 SER A 347 REMARK 465 VAL A 348 REMARK 465 LYS A 349 REMARK 465 TYR A 350 REMARK 465 ALA A 483 REMARK 465 GLU A 484 REMARK 465 ALA A 485 REMARK 465 ALA A 486 REMARK 465 PRO A 487 REMARK 465 THR A 488 REMARK 465 GLU A 489 REMARK 465 SER A 490 REMARK 465 ASP A 491 REMARK 465 GLN A 492 REMARK 465 GLU A 522 REMARK 465 GLU A 523 REMARK 465 GLU A 524 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 204 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLN A 216 CG CD OE1 NE2 REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 LYS A 262 CG CD CE NZ REMARK 470 VAL A 275 CG1 CG2 REMARK 470 SER A 284 OG REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 LYS A 305 CG CD CE NZ REMARK 470 GLU A 336 CG CD OE1 OE2 REMARK 470 LEU A 376 CG CD1 CD2 REMARK 470 PHE A 481 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 482 CG OD1 ND2 REMARK 470 MET A 493 CG SD CE REMARK 470 GLU A 497 CG CD OE1 OE2 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 TRP A 154 34.57 -90.50 REMARK 500 ASN A 202 50.86 -105.14 REMARK 500 ASN A 321 -143.17 59.92 REMARK 500 ASP A 444 -116.20 52.34 REMARK 500 SER A 450 -157.83 -133.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 402 -10.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 789 DISTANCE = 6.33 ANGSTROMS DBREF 8P14 A 149 399 UNP Q96RU2 UBP28_HUMAN 149 399 DBREF 8P14 A 406 524 UNP Q96RU2 UBP28_HUMAN 580 698 SEQADV 8P14 GLY A 148 UNP Q96RU2 EXPRESSION TAG SEQADV 8P14 GLY A 400 UNP Q96RU2 LINKER SEQADV 8P14 SER A 401 UNP Q96RU2 LINKER SEQADV 8P14 GLY A 402 UNP Q96RU2 LINKER SEQADV 8P14 SER A 403 UNP Q96RU2 LINKER SEQADV 8P14 GLY A 404 UNP Q96RU2 LINKER SEQADV 8P14 SER A 405 UNP Q96RU2 LINKER SEQRES 1 A 377 GLY PRO ASN PRO ASN ASP TRP ARG ARG VAL ASP GLY TRP SEQRES 2 A 377 PRO VAL GLY LEU LYS ASN VAL GLY ASN THR CYS TRP PHE SEQRES 3 A 377 SER ALA VAL ILE GLN SER LEU PHE GLN LEU PRO GLU PHE SEQRES 4 A 377 ARG ARG LEU VAL LEU SER TYR SER LEU PRO GLN ASN VAL SEQRES 5 A 377 LEU GLU ASN CYS ARG SER HIS THR GLU LYS ARG ASN ILE SEQRES 6 A 377 MET PHE MET GLN GLU LEU GLN TYR LEU PHE ALA LEU MET SEQRES 7 A 377 MET GLY SER ASN ARG LYS PHE VAL ASP PRO SER ALA ALA SEQRES 8 A 377 LEU ASP LEU LEU LYS GLY ALA PHE ARG SER SER GLU GLU SEQRES 9 A 377 GLN GLN GLN ASP VAL SER GLU PHE THR HIS LYS LEU LEU SEQRES 10 A 377 ASP TRP LEU GLU ASP ALA PHE GLN LEU ALA VAL ASN VAL SEQRES 11 A 377 ASN SER PRO ARG ASN LYS SER GLU ASN PRO MET VAL GLN SEQRES 12 A 377 LEU PHE TYR GLY THR PHE LEU THR GLU GLY VAL ARG GLU SEQRES 13 A 377 GLY LYS PRO PHE CYS ASN ASN GLU THR PHE GLY GLN TYR SEQRES 14 A 377 PRO LEU GLN VAL ASN GLY TYR ARG ASN LEU ASP GLU CYS SEQRES 15 A 377 LEU GLU GLY ALA MET VAL GLU GLY ASP VAL GLU LEU LEU SEQRES 16 A 377 PRO SER ASP HIS SER VAL LYS TYR GLY GLN GLU ARG TRP SEQRES 17 A 377 PHE THR LYS LEU PRO PRO VAL LEU THR PHE GLU LEU SER SEQRES 18 A 377 ARG PHE GLU PHE ASN GLN SER LEU GLY GLN PRO GLU LYS SEQRES 19 A 377 ILE HIS ASN LYS LEU GLU PHE PRO GLN ILE ILE TYR MET SEQRES 20 A 377 ASP ARG TYR MET TYR GLY SER GLY SER GLY SER ARG GLN SEQRES 21 A 377 VAL PRO TYR ARG LEU HIS ALA VAL LEU VAL HIS GLU GLY SEQRES 22 A 377 GLN ALA ASN ALA GLY HIS TYR TRP ALA TYR ILE TYR ASN SEQRES 23 A 377 GLN PRO ARG GLN SER TRP LEU LYS TYR ASN ASP ILE SER SEQRES 24 A 377 VAL THR GLU SER SER TRP GLU GLU VAL GLU ARG ASP SER SEQRES 25 A 377 TYR GLY GLY LEU ARG ASN VAL SER ALA TYR CYS LEU MET SEQRES 26 A 377 TYR ILE ASN ASP LYS LEU PRO TYR PHE ASN ALA GLU ALA SEQRES 27 A 377 ALA PRO THR GLU SER ASP GLN MET SER GLU VAL GLU ALA SEQRES 28 A 377 LEU SER VAL GLU LEU LYS HIS TYR ILE GLN GLU ASP ASN SEQRES 29 A 377 TRP ARG PHE GLU GLN GLU VAL GLU GLU TRP GLU GLU GLU HET VIS A 601 27 HET CL A 602 1 HET CL A 603 1 HET CL A 604 1 HET CL A 605 1 HETNAM VIS 2-CHLORANYL-~{N}-(4-CHLORANYL-3-PYRIDIN-2-YL-PHENYL)-4- HETNAM 2 VIS METHYLSULFONYL-BENZAMIDE HETNAM CL CHLORIDE ION FORMUL 2 VIS C19 H14 CL2 N2 O3 S FORMUL 3 CL 4(CL 1-) FORMUL 7 HOH *89(H2 O) HELIX 1 AA1 THR A 170 GLN A 182 1 13 HELIX 2 AA2 LEU A 183 SER A 192 1 10 HELIX 3 AA3 PRO A 196 GLU A 201 1 6 HELIX 4 AA4 SER A 205 SER A 228 1 24 HELIX 5 AA5 PRO A 235 LYS A 243 1 9 HELIX 6 AA6 VAL A 256 ASN A 276 1 21 HELIX 7 AA7 ASN A 286 TYR A 293 1 8 HELIX 8 AA8 ASN A 325 MET A 334 1 10 HELIX 9 AA9 ASP A 395 MET A 398 5 4 HELIX 10 AB1 SER A 451 TYR A 460 1 10 HELIX 11 AB2 LEU A 478 ASN A 482 5 5 HELIX 12 AB3 GLU A 495 LEU A 499 5 5 HELIX 13 AB4 SER A 500 TRP A 521 1 22 SHEET 1 AA1 2 GLY A 163 LEU A 164 0 SHEET 2 AA1 2 PHE A 232 VAL A 233 1 O VAL A 233 N GLY A 163 SHEET 1 AA2 3 LYS A 305 PHE A 313 0 SHEET 2 AA2 3 GLY A 294 ARG A 302 -1 N GLY A 300 O PHE A 307 SHEET 3 AA2 3 GLU A 353 LYS A 358 -1 O GLU A 353 N GLU A 299 SHEET 1 AA3 5 TYR A 316 GLN A 319 0 SHEET 2 AA3 5 VAL A 362 SER A 368 1 O GLU A 366 N LEU A 318 SHEET 3 AA3 5 VAL A 466 ASN A 475 -1 O TYR A 473 N LEU A 363 SHEET 4 AA3 5 PRO A 409 GLU A 419 -1 N HIS A 413 O MET A 472 SHEET 5 AA3 5 ILE A 391 TYR A 393 -1 N ILE A 392 O TYR A 410 SHEET 1 AA4 7 TYR A 316 GLN A 319 0 SHEET 2 AA4 7 VAL A 362 SER A 368 1 O GLU A 366 N LEU A 318 SHEET 3 AA4 7 VAL A 466 ASN A 475 -1 O TYR A 473 N LEU A 363 SHEET 4 AA4 7 PRO A 409 GLU A 419 -1 N HIS A 413 O MET A 472 SHEET 5 AA4 7 HIS A 426 ASN A 433 -1 O TYR A 430 N VAL A 415 SHEET 6 AA4 7 SER A 438 ASN A 443 -1 O SER A 438 N ASN A 433 SHEET 7 AA4 7 SER A 446 GLU A 449 -1 O THR A 448 N LYS A 441 SHEET 1 AA5 2 PHE A 370 ASN A 373 0 SHEET 2 AA5 2 GLN A 378 LYS A 381 -1 O GLU A 380 N GLU A 371 CRYST1 106.634 106.634 329.857 90.00 90.00 120.00 H 3 2 18 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 0.009378 0.005414 0.000000 0.00000 SCALE2 0.000000 0.010829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003032 0.00000