HEADER HYDROLASE/HYDROLASE INHIBITOR 03-FEB-22 7TUO TITLE CRYSTAL STRUCTURE ANALYSIS OF HUMAN USP28 COMPLEX WITH A COMPOUND 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: 3.4.19.12,3.4.19.12; COMPND 7 ENGINEERED: YES 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DEUBIQUITINASE, INHIBITOR, PROTEIN-INHIBITOR COMPLEX, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.-S.SEO,S.DHE-PAGANON REVDAT 2 25-OCT-23 7TUO 1 REMARK REVDAT 1 15-FEB-23 7TUO 0 JRNL AUTH H.-S.SEO,S.DHE-PAGANON JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF HUMAN USP28 COMPLEX WITH A JRNL TITL 2 COMPOUND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 36269 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1824 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 81.0600 - 4.6100 1.00 2774 152 0.1686 0.1692 REMARK 3 2 4.6100 - 3.6600 1.00 2668 170 0.1427 0.1581 REMARK 3 3 3.6500 - 3.2000 1.00 2676 129 0.1474 0.1961 REMARK 3 4 3.1900 - 2.9000 1.00 2614 178 0.1887 0.2319 REMARK 3 5 2.9000 - 2.7000 1.00 2647 139 0.1840 0.2303 REMARK 3 6 2.6900 - 2.5400 1.00 2655 122 0.1981 0.2563 REMARK 3 7 2.5400 - 2.4100 1.00 2657 125 0.2221 0.2334 REMARK 3 8 2.4100 - 2.3000 1.00 2633 138 0.2076 0.2597 REMARK 3 9 2.3000 - 2.2200 1.00 2646 112 0.2079 0.2099 REMARK 3 10 2.2200 - 2.1400 1.00 2603 152 0.1994 0.2735 REMARK 3 11 2.1400 - 2.0700 1.00 2624 133 0.2243 0.2473 REMARK 3 12 2.0700 - 2.0100 1.00 2626 133 0.2479 0.2781 REMARK 3 13 2.0100 - 1.9600 1.00 2622 141 0.3092 0.3463 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) : 23.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.60 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 : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 149 THROUGH 325 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5407 29.6779 -15.6589 REMARK 3 T TENSOR REMARK 3 T11: 0.2998 T22: 0.3405 REMARK 3 T33: 0.3748 T12: 0.0586 REMARK 3 T13: 0.0124 T23: 0.0655 REMARK 3 L TENSOR REMARK 3 L11: 2.0589 L22: 2.3187 REMARK 3 L33: 1.1883 L12: 1.0571 REMARK 3 L13: -0.2703 L23: 0.0266 REMARK 3 S TENSOR REMARK 3 S11: -0.0098 S12: 0.1314 S13: 0.3267 REMARK 3 S21: -0.1960 S22: 0.0402 S23: 0.2159 REMARK 3 S31: -0.2206 S32: -0.1025 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 326 THROUGH 368 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0236 9.2733 -17.7520 REMARK 3 T TENSOR REMARK 3 T11: 0.3647 T22: 0.4576 REMARK 3 T33: 0.3448 T12: -0.0650 REMARK 3 T13: -0.0016 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.3877 L22: 0.2363 REMARK 3 L33: 0.5524 L12: -0.0466 REMARK 3 L13: -0.4267 L23: -0.0877 REMARK 3 S TENSOR REMARK 3 S11: -0.0753 S12: 0.2608 S13: -0.0984 REMARK 3 S21: 0.0803 S22: 0.0583 S23: 0.2910 REMARK 3 S31: 0.2451 S32: -0.5032 S33: 0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 369 THROUGH 582 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.1855 9.6094 -10.1027 REMARK 3 T TENSOR REMARK 3 T11: 0.3148 T22: 0.4151 REMARK 3 T33: 0.3491 T12: 0.0173 REMARK 3 T13: -0.0314 T23: 0.0280 REMARK 3 L TENSOR REMARK 3 L11: 1.0410 L22: 2.1248 REMARK 3 L33: 1.9588 L12: 0.7802 REMARK 3 L13: -0.5320 L23: -0.7305 REMARK 3 S TENSOR REMARK 3 S11: 0.0223 S12: 0.2476 S13: -0.0545 REMARK 3 S21: -0.0256 S22: 0.0455 S23: 0.5636 REMARK 3 S31: 0.0424 S32: -0.5748 S33: 0.0076 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 583 THROUGH 625 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4528 21.6193 -3.2172 REMARK 3 T TENSOR REMARK 3 T11: 0.2801 T22: 0.3015 REMARK 3 T33: 0.2933 T12: 0.0033 REMARK 3 T13: 0.0237 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 1.6390 L22: 2.1844 REMARK 3 L33: 2.2407 L12: 1.6915 REMARK 3 L13: 0.6641 L23: -0.0824 REMARK 3 S TENSOR REMARK 3 S11: 0.0922 S12: -0.2037 S13: 0.3319 REMARK 3 S21: 0.2147 S22: -0.0348 S23: 0.0530 REMARK 3 S31: -0.2338 S32: 0.0716 S33: 0.0011 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 626 THROUGH 674 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4681 18.1124 -8.9695 REMARK 3 T TENSOR REMARK 3 T11: 0.3267 T22: 0.3507 REMARK 3 T33: 0.3645 T12: 0.0106 REMARK 3 T13: 0.0123 T23: 0.0223 REMARK 3 L TENSOR REMARK 3 L11: 0.6099 L22: 0.7700 REMARK 3 L33: 0.4035 L12: 0.5090 REMARK 3 L13: -0.1427 L23: -0.4693 REMARK 3 S TENSOR REMARK 3 S11: 0.0226 S12: -0.1066 S13: 0.0915 REMARK 3 S21: 0.0852 S22: -0.0285 S23: -0.0723 REMARK 3 S31: -0.1582 S32: 0.1767 S33: 0.0010 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 675 THROUGH 699 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.3738 45.5454 -4.7575 REMARK 3 T TENSOR REMARK 3 T11: 0.4924 T22: 0.5130 REMARK 3 T33: 0.6206 T12: -0.0473 REMARK 3 T13: 0.0853 T23: -0.0761 REMARK 3 L TENSOR REMARK 3 L11: 1.2403 L22: 1.0437 REMARK 3 L33: 0.8886 L12: -0.2106 REMARK 3 L13: -0.1482 L23: -0.5946 REMARK 3 S TENSOR REMARK 3 S11: 0.3664 S12: -0.4589 S13: 0.6978 REMARK 3 S21: 0.2325 S22: 0.0959 S23: 0.1153 REMARK 3 S31: -0.9787 S32: -0.2670 S33: 0.0011 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 7TUO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000262938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 81.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 6HEH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M SODIUM MALEIC ACID, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 57.32000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.32000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.32000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.32000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.32000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.32000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 57.32000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 57.32000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 57.32000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 57.32000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 57.32000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 57.32000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 57.32000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 57.32000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 57.32000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 57.32000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 57.32000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 57.32000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1081 LIES ON A SPECIAL POSITION. 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 SER A 148 REMARK 465 GLN A 197 REMARK 465 ASN A 198 REMARK 465 VAL A 199 REMARK 465 LEU A 200 REMARK 465 GLU A 201 REMARK 465 ASN A 202 REMARK 465 CYS A 203 REMARK 465 ARG A 204 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 300 REMARK 465 VAL A 301 REMARK 465 ARG A 302 REMARK 465 GLU A 303 REMARK 465 GLY A 304 REMARK 465 LYS A 305 REMARK 465 PRO A 306 REMARK 465 GLU A 336 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 GLY A 351 REMARK 465 GLY A 576 REMARK 465 SER A 577 REMARK 465 GLY A 578 REMARK 465 ALA A 659 REMARK 465 ALA A 660 REMARK 465 PRO A 661 REMARK 465 THR A 662 REMARK 465 GLU A 663 REMARK 465 SER A 664 REMARK 465 ASP A 665 REMARK 465 SER A 700 REMARK 465 CYS A 701 REMARK 465 LYS A 702 REMARK 465 ILE A 703 REMARK 465 GLN A 704 REMARK 465 LEU A 705 REMARK 465 ASN A 706 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 ASP A 158 CG OD1 OD2 REMARK 470 ASN A 169 CG OD1 ND2 REMARK 470 HIS A 206 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 PHE A 307 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 309 CG OD1 ND2 REMARK 470 GLN A 352 CG CD OE1 NE2 REMARK 470 SER A 375 OG REMARK 470 LEU A 376 CG CD1 CD2 REMARK 470 GLN A 666 CG CD OE1 NE2 REMARK 470 GLU A 697 CG CD OE1 OE2 REMARK 470 GLU A 698 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 231 O HOH A 901 1.93 REMARK 500 OD2 ASP A 255 O HOH A 902 1.98 REMARK 500 O HOH A 902 O HOH A 1067 2.05 REMARK 500 OG1 THR A 298 O HOH A 903 2.07 REMARK 500 O HOH A 1050 O HOH A 1072 2.12 REMARK 500 O HOH A 981 O HOH A 1017 2.12 REMARK 500 OE1 GLU A 331 O HOH A 904 2.15 REMARK 500 O HOH A 1061 O HOH A 1083 2.16 REMARK 500 OE1 GLU A 683 O HOH A 905 2.16 REMARK 500 O HOH A 918 O HOH A 1046 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 921 O HOH A 1062 5555 1.85 REMARK 500 O HOH A 938 O HOH A 1087 6555 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 183 CA - CB - CG ANGL. DEV. = 22.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 321 -136.92 58.16 REMARK 500 MET A 334 4.01 -69.05 REMARK 500 ALA A 598 -149.14 -150.67 REMARK 500 ASP A 618 -120.69 55.82 REMARK 500 REMARK 500 REMARK: NULL DBREF 7TUO A 149 399 UNP Q96RU2 UBP28_HUMAN 149 399 DBREF 7TUO A 580 703 UNP Q96RU2 UBP28_HUMAN 580 703 SEQADV 7TUO SER A 148 UNP Q96RU2 EXPRESSION TAG SEQADV 7TUO GLY A 400 UNP Q96RU2 LINKER SEQADV 7TUO SER A 401 UNP Q96RU2 LINKER SEQADV 7TUO GLY A 576 UNP Q96RU2 LINKER SEQADV 7TUO SER A 577 UNP Q96RU2 LINKER SEQADV 7TUO GLY A 578 UNP Q96RU2 LINKER SEQADV 7TUO SER A 579 UNP Q96RU2 LINKER SEQADV 7TUO GLN A 704 UNP Q96RU2 EXPRESSION TAG SEQADV 7TUO LEU A 705 UNP Q96RU2 EXPRESSION TAG SEQADV 7TUO ASN A 706 UNP Q96RU2 EXPRESSION TAG SEQRES 1 A 385 SER PRO ASN PRO ASN ASP TRP ARG ARG VAL ASP GLY TRP SEQRES 2 A 385 PRO VAL GLY LEU LYS ASN VAL GLY ASN THR CYS TRP PHE SEQRES 3 A 385 SER ALA VAL ILE GLN SER LEU PHE GLN LEU PRO GLU PHE SEQRES 4 A 385 ARG ARG LEU VAL LEU SER TYR SER LEU PRO GLN ASN VAL SEQRES 5 A 385 LEU GLU ASN CYS ARG SER HIS THR GLU LYS ARG ASN ILE SEQRES 6 A 385 MET PHE MET GLN GLU LEU GLN TYR LEU PHE ALA LEU MET SEQRES 7 A 385 MET GLY SER ASN ARG LYS PHE VAL ASP PRO SER ALA ALA SEQRES 8 A 385 LEU ASP LEU LEU LYS GLY ALA PHE ARG SER SER GLU GLU SEQRES 9 A 385 GLN GLN GLN ASP VAL SER GLU PHE THR HIS LYS LEU LEU SEQRES 10 A 385 ASP TRP LEU GLU ASP ALA PHE GLN LEU ALA VAL ASN VAL SEQRES 11 A 385 ASN SER PRO ARG ASN LYS SER GLU ASN PRO MET VAL GLN SEQRES 12 A 385 LEU PHE TYR GLY THR PHE LEU THR GLU GLY VAL ARG GLU SEQRES 13 A 385 GLY LYS PRO PHE CYS ASN ASN GLU THR PHE GLY GLN TYR SEQRES 14 A 385 PRO LEU GLN VAL ASN GLY TYR ARG ASN LEU ASP GLU CYS SEQRES 15 A 385 LEU GLU GLY ALA MET VAL GLU GLY ASP VAL GLU LEU LEU SEQRES 16 A 385 PRO SER ASP HIS SER VAL LYS TYR GLY GLN GLU ARG TRP SEQRES 17 A 385 PHE THR LYS LEU PRO PRO VAL LEU THR PHE GLU LEU SER SEQRES 18 A 385 ARG PHE GLU PHE ASN GLN SER LEU GLY GLN PRO GLU LYS SEQRES 19 A 385 ILE HIS ASN LYS LEU GLU PHE PRO GLN ILE ILE TYR MET SEQRES 20 A 385 ASP ARG TYR MET TYR GLY SER GLY SER GLY SER ARG GLN SEQRES 21 A 385 VAL PRO TYR ARG LEU HIS ALA VAL LEU VAL HIS GLU GLY SEQRES 22 A 385 GLN ALA ASN ALA GLY HIS TYR TRP ALA TYR ILE TYR ASN SEQRES 23 A 385 GLN PRO ARG GLN SER TRP LEU LYS TYR ASN ASP ILE SER SEQRES 24 A 385 VAL THR GLU SER SER TRP GLU GLU VAL GLU ARG ASP SER SEQRES 25 A 385 TYR GLY GLY LEU ARG ASN VAL SER ALA TYR CYS LEU MET SEQRES 26 A 385 TYR ILE ASN ASP LYS LEU PRO TYR PHE ASN ALA GLU ALA SEQRES 27 A 385 ALA PRO THR GLU SER ASP GLN MET SER GLU VAL GLU ALA SEQRES 28 A 385 LEU SER VAL GLU LEU LYS HIS TYR ILE GLN GLU ASP ASN SEQRES 29 A 385 TRP ARG PHE GLU GLN GLU VAL GLU GLU TRP GLU GLU GLU SEQRES 30 A 385 GLN SER CYS LYS ILE GLN LEU ASN HET KL9 A 801 57 HET KL9 A 802 57 HET CL A 803 1 HETNAM KL9 7-AMINO-N-(2-{4-[(1R,3S,5S)-8-AZABICYCLO[3.2.1]OCTAN-3- HETNAM 2 KL9 YL]PHENYL}ETHYL)-3-METHYLTHIENO[2,3-B]PYRAZINE-6- HETNAM 3 KL9 CARBOXAMIDE HETNAM CL CHLORIDE ION FORMUL 2 KL9 2(C23 H27 N5 O S) FORMUL 4 CL CL 1- FORMUL 5 HOH *205(H2 O) HELIX 1 AA1 ASN A 150 ARG A 155 5 6 HELIX 2 AA2 THR A 170 GLN A 182 1 13 HELIX 3 AA3 LEU A 183 SER A 192 1 10 HELIX 4 AA4 HIS A 206 SER A 228 1 23 HELIX 5 AA5 PRO A 235 ALA A 245 1 11 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 625 TYR A 634 1 10 HELIX 11 AB2 MET A 667 ALA A 672 1 6 HELIX 12 AB3 SER A 674 GLU A 698 1 25 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 ASN A 309 PHE A 313 0 SHEET 2 AA2 3 GLY A 294 GLU A 299 -1 N THR A 298 O ASN A 309 SHEET 3 AA2 3 GLU A 353 LYS A 358 -1 O TRP A 355 N LEU A 297 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 640 ASN A 649 -1 O TYR A 647 N LEU A 363 SHEET 4 AA3 5 PRO A 583 GLU A 593 -1 N HIS A 587 O MET A 646 SHEET 5 AA3 5 ILE A 391 TYR A 393 -1 N ILE A 392 O TYR A 584 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 640 ASN A 649 -1 O TYR A 647 N LEU A 363 SHEET 4 AA4 7 PRO A 583 GLU A 593 -1 N HIS A 587 O MET A 646 SHEET 5 AA4 7 HIS A 600 ASN A 607 -1 O TRP A 602 N VAL A 591 SHEET 6 AA4 7 SER A 612 ASN A 617 -1 O TYR A 616 N ALA A 603 SHEET 7 AA4 7 SER A 620 GLU A 623 -1 O THR A 622 N LYS A 615 SHEET 1 AA5 2 PHE A 370 ASN A 373 0 SHEET 2 AA5 2 GLN A 378 LYS A 381 -1 O GLN A 378 N ASN A 373 CRYST1 114.640 114.640 114.640 90.00 90.00 90.00 P 21 3 12 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 0.008723 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008723 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008723 0.00000