HEADER HYDROLASE 06-MAY-18 6GH9 TITLE USP15 CATALYTIC DOMAIN IN COMPLEX WITH SMALL MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 15,UBIQUITIN THIOESTERASE 15, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 15,UNPH-2,UNPH4; COMPND 6 EC: 3.4.19.12; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CATALYTIC CORE REGION (USP15-D1D2) WITH THE INSERT COMPND 9 HARBOURING A PREDICTED UBL DOMAIN REPLACED BY A SHORT LINKER (BASED COMPND 10 ON THE USP8 STRUCTURE PDB ID: 2GFO),CATALYTIC CORE REGION (USP15- COMPND 11 D1D2) WITH THE INSERT HARBOURING A PREDICTED UBL DOMAIN REPLACED BY A COMPND 12 SHORT LINKER (BASED ON THE USP8 STRUCTURE PDB ID: 2GFO),CATALYTIC COMPND 13 CORE REGION (USP15-D1D2) WITH THE INSERT HARBOURING A PREDICTED UBL COMPND 14 DOMAIN REPLACED BY A SHORT LINKER (BASED ON THE USP8 STRUCTURE PDB COMPND 15 ID: 2GFO),CATALYTIC CORE REGION (USP15-D1D2) WITH THE INSERT COMPND 16 HARBOURING A PREDICTED UBL DOMAIN REPLACED BY A SHORT LINKER (BASED COMPND 17 ON THE USP8 STRUCTURE PDB ID: 2GFO) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP15, KIAA0529; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEASE, UBIQUITIN, UBIQUITIN SPECIFIC PROTEASE, INHIBITOR, KEYWDS 2 MITOXANTRONE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.WARD,H.E.GRATTON,S.G.CAULTON,J.EMSLEY,I.DREVENY REVDAT 4 17-JAN-24 6GH9 1 HETSYN REVDAT 3 21-NOV-18 6GH9 1 JRNL REVDAT 2 03-OCT-18 6GH9 1 JRNL REVDAT 1 26-SEP-18 6GH9 0 JRNL AUTH S.J.WARD,H.E.GRATTON,P.INDRAYUDHA,C.MICHAVILA, JRNL AUTH 2 R.MUKHOPADHYAY,S.K.MAURER,S.G.CAULTON,J.EMSLEY,I.DREVENY JRNL TITL THE STRUCTURE OF THE DEUBIQUITINASE USP15 REVEALS A JRNL TITL 2 MISALIGNED CATALYTIC TRIAD AND AN OPEN UBIQUITIN-BINDING JRNL TITL 3 CHANNEL. JRNL REF J. BIOL. CHEM. V. 293 17362 2018 JRNL REFN ESSN 1083-351X JRNL PMID 30228188 JRNL DOI 10.1074/JBC.RA118.003857 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 42747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 2035 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 62.0973 - 5.1536 0.99 2762 140 0.1967 0.2453 REMARK 3 2 5.1536 - 4.0908 0.99 2737 153 0.1521 0.1811 REMARK 3 3 4.0908 - 3.5737 0.99 2753 119 0.1667 0.1973 REMARK 3 4 3.5737 - 3.2470 0.99 2709 152 0.1833 0.2550 REMARK 3 5 3.2470 - 3.0143 0.99 2736 129 0.2050 0.2987 REMARK 3 6 3.0143 - 2.8366 0.99 2738 124 0.2130 0.2791 REMARK 3 7 2.8366 - 2.6945 0.99 2673 149 0.2360 0.2750 REMARK 3 8 2.6945 - 2.5772 0.99 2744 121 0.2223 0.2732 REMARK 3 9 2.5772 - 2.4780 0.99 2694 140 0.2409 0.2929 REMARK 3 10 2.4780 - 2.3925 0.99 2674 144 0.2459 0.2753 REMARK 3 11 2.3925 - 2.3177 0.99 2726 140 0.2556 0.3032 REMARK 3 12 2.3177 - 2.2514 0.99 2681 161 0.2757 0.3363 REMARK 3 13 2.2514 - 2.1921 0.98 2688 125 0.3017 0.3515 REMARK 3 14 2.1921 - 2.1387 0.98 2701 102 0.3240 0.4545 REMARK 3 15 2.1387 - 2.0900 0.98 2696 136 0.3383 0.3724 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.03 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 254 THROUGH 385 ) REMARK 3 ORIGIN FOR THE GROUP (A): -87.7127 15.3377 38.7510 REMARK 3 T TENSOR REMARK 3 T11: 0.2668 T22: 0.5444 REMARK 3 T33: 0.2679 T12: -0.0727 REMARK 3 T13: -0.0203 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 6.5142 L22: 2.3137 REMARK 3 L33: 3.3479 L12: -1.5042 REMARK 3 L13: -1.2697 L23: -0.0314 REMARK 3 S TENSOR REMARK 3 S11: 0.0170 S12: -0.2206 S13: -0.0882 REMARK 3 S21: 0.2512 S22: 0.0577 S23: 0.1666 REMARK 3 S31: 0.0307 S32: -0.1107 S33: -0.0445 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 386 THROUGH 913 ) REMARK 3 ORIGIN FOR THE GROUP (A): -78.9844 28.3770 27.3030 REMARK 3 T TENSOR REMARK 3 T11: 0.2839 T22: 0.5782 REMARK 3 T33: 0.2973 T12: 0.0003 REMARK 3 T13: 0.0216 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 3.2681 L22: 3.0943 REMARK 3 L33: 2.5003 L12: -0.6357 REMARK 3 L13: -0.4054 L23: -0.5520 REMARK 3 S TENSOR REMARK 3 S11: 0.0934 S12: 0.3265 S13: 0.4162 REMARK 3 S21: 0.0633 S22: 0.0110 S23: -0.2109 REMARK 3 S31: -0.3237 S32: 0.1629 S33: -0.1060 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 254 THROUGH 279 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.4348 9.0974 6.2723 REMARK 3 T TENSOR REMARK 3 T11: 0.2766 T22: 0.6523 REMARK 3 T33: 0.3798 T12: 0.0358 REMARK 3 T13: -0.0350 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 2.7305 L22: 3.4660 REMARK 3 L33: 6.7663 L12: 3.0829 REMARK 3 L13: 0.2608 L23: 0.2036 REMARK 3 S TENSOR REMARK 3 S11: 0.0556 S12: -0.4197 S13: -0.4309 REMARK 3 S21: 0.5924 S22: -0.3555 S23: -0.5630 REMARK 3 S31: -0.0970 S32: 0.6247 S33: 0.2277 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 280 THROUGH 366 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.7238 18.7720 8.6431 REMARK 3 T TENSOR REMARK 3 T11: 0.2961 T22: 0.4860 REMARK 3 T33: 0.2772 T12: -0.0935 REMARK 3 T13: -0.0085 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 7.0927 L22: 2.7260 REMARK 3 L33: 3.8184 L12: -1.0440 REMARK 3 L13: -0.3065 L23: 0.8590 REMARK 3 S TENSOR REMARK 3 S11: 0.0980 S12: -0.8170 S13: 0.4182 REMARK 3 S21: 0.4313 S22: -0.0286 S23: -0.1289 REMARK 3 S31: -0.0202 S32: 0.3276 S33: -0.0367 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 367 THROUGH 385 ) REMARK 3 ORIGIN FOR THE GROUP (A): -72.0149 20.4779 2.4198 REMARK 3 T TENSOR REMARK 3 T11: 0.4473 T22: 0.8782 REMARK 3 T33: 0.5133 T12: 0.0452 REMARK 3 T13: 0.0928 T23: -0.0451 REMARK 3 L TENSOR REMARK 3 L11: 3.1638 L22: 1.3388 REMARK 3 L33: 5.6769 L12: -1.8044 REMARK 3 L13: -0.2009 L23: 0.5924 REMARK 3 S TENSOR REMARK 3 S11: 0.0450 S12: -0.8211 S13: 0.3642 REMARK 3 S21: 0.3004 S22: -0.4523 S23: 0.8014 REMARK 3 S31: 0.4816 S32: -1.8159 S33: 0.3697 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 386 THROUGH 911 ) REMARK 3 ORIGIN FOR THE GROUP (A): -55.9220 4.6517 -5.2422 REMARK 3 T TENSOR REMARK 3 T11: 0.2499 T22: 0.4253 REMARK 3 T33: 0.3132 T12: -0.0048 REMARK 3 T13: 0.0171 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 6.1526 L22: 2.2870 REMARK 3 L33: 2.5263 L12: -1.6353 REMARK 3 L13: 0.2790 L23: 0.5751 REMARK 3 S TENSOR REMARK 3 S11: 0.0896 S12: 0.4202 S13: -0.7667 REMARK 3 S21: 0.0455 S22: -0.0300 S23: 0.2588 REMARK 3 S31: 0.2088 S32: -0.1285 S33: -0.0805 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 254 THROUGH 311 OR REMARK 3 RESID 313 THROUGH 771 OR RESID 789 REMARK 3 THROUGH 856 OR RESID 862 THROUGH 911)) REMARK 3 SELECTION : (CHAIN B AND (RESID 254 THROUGH 311 OR REMARK 3 RESID 313 THROUGH 753 OR RESID 756 REMARK 3 THROUGH 911)) REMARK 3 ATOM PAIRS NUMBER : 2896 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1200009928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97951 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.29 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42810 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 62.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 1.61900 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: 2Y6E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 14% MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 47.19500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 PHE A 344 REMARK 465 SER A 345 REMARK 465 GLY A 346 REMARK 465 TYR A 347 REMARK 465 GLN A 348 REMARK 465 GLN A 349 REMARK 465 GLN A 350 REMARK 465 ASP A 351 REMARK 465 CYS A 352 REMARK 465 SER A 753 REMARK 465 THR A 754 REMARK 465 TYR A 811 REMARK 465 SER A 812 REMARK 465 ARG A 813 REMARK 465 TYR A 814 REMARK 465 MET A 815 REMARK 465 ARG A 816 REMARK 465 PRO A 914 REMARK 465 LEU A 915 REMARK 465 ASP A 916 REMARK 465 ARG A 917 REMARK 465 GLU A 918 REMARK 465 THR A 919 REMARK 465 ALA A 920 REMARK 465 ALA A 921 REMARK 465 ALA A 922 REMARK 465 LEU A 923 REMARK 465 GLU A 924 REMARK 465 HIS A 925 REMARK 465 HIS A 926 REMARK 465 HIS A 927 REMARK 465 HIS A 928 REMARK 465 HIS A 929 REMARK 465 HIS A 930 REMARK 465 PHE B 344 REMARK 465 SER B 345 REMARK 465 GLY B 346 REMARK 465 TYR B 347 REMARK 465 GLN B 348 REMARK 465 GLN B 349 REMARK 465 GLN B 350 REMARK 465 ASP B 351 REMARK 465 CYS B 352 REMARK 465 LEU B 772 REMARK 465 GLY B 773 REMARK 465 ALA B 774 REMARK 465 GLU B 775 REMARK 465 ASP B 776 REMARK 465 PRO B 777 REMARK 465 TRP B 778 REMARK 465 TYR B 779 REMARK 465 CYS B 780 REMARK 465 PRO B 781 REMARK 465 ASN B 782 REMARK 465 CYS B 783 REMARK 465 LYS B 784 REMARK 465 GLU B 785 REMARK 465 HIS B 786 REMARK 465 GLN B 787 REMARK 465 GLN B 788 REMARK 465 TYR B 811 REMARK 465 SER B 812 REMARK 465 ARG B 813 REMARK 465 TYR B 814 REMARK 465 MET B 815 REMARK 465 ARG B 816 REMARK 465 GLY B 856 REMARK 465 GLY B 857 REMARK 465 MET B 858 REMARK 465 GLY B 859 REMARK 465 GLY B 860 REMARK 465 PHE B 912 REMARK 465 PHE B 913 REMARK 465 PRO B 914 REMARK 465 LEU B 915 REMARK 465 ASP B 916 REMARK 465 ARG B 917 REMARK 465 GLU B 918 REMARK 465 THR B 919 REMARK 465 ALA B 920 REMARK 465 ALA B 921 REMARK 465 ALA B 922 REMARK 465 LEU B 923 REMARK 465 GLU B 924 REMARK 465 HIS B 925 REMARK 465 HIS B 926 REMARK 465 HIS B 927 REMARK 465 HIS B 928 REMARK 465 HIS B 929 REMARK 465 HIS B 930 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 THR A 268 63.60 27.98 REMARK 500 PHE A 270 -17.95 74.93 REMARK 500 PRO A 330 35.28 -92.09 REMARK 500 ASP A 382 -122.91 53.26 REMARK 500 GLN A 787 -164.33 -177.88 REMARK 500 CYS A 844 69.01 39.06 REMARK 500 ASP A 880 -124.92 52.90 REMARK 500 GLU B 255 15.38 50.68 REMARK 500 PHE B 270 -20.15 75.94 REMARK 500 PRO B 330 33.15 -92.36 REMARK 500 ALA B 423 18.05 54.79 REMARK 500 SER B 753 89.67 -67.08 REMARK 500 ASP B 820 34.13 -94.91 REMARK 500 ASP B 880 -125.80 51.47 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 B1073 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH B1074 DISTANCE = 7.44 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 419 SG REMARK 620 2 CYS A 422 SG 118.2 REMARK 620 3 CYS A 780 SG 115.6 96.1 REMARK 620 4 CYS A 783 SG 132.4 97.4 88.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MIX A 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GHA RELATED DB: PDB DBREF 6GH9 A 255 439 UNP Q9Y4E8 UBP15_HUMAN 255 439 DBREF 6GH9 A 757 922 UNP Q9Y4E8 UBP15_HUMAN 757 922 DBREF 6GH9 B 255 439 UNP Q9Y4E8 UBP15_HUMAN 255 439 DBREF 6GH9 B 757 922 UNP Q9Y4E8 UBP15_HUMAN 757 922 SEQADV 6GH9 MET A 254 UNP Q9Y4E8 INITIATING METHIONINE SEQADV 6GH9 ALA A 440 UNP Q9Y4E8 LINKER SEQADV 6GH9 SER A 753 UNP Q9Y4E8 LINKER SEQADV 6GH9 THR A 754 UNP Q9Y4E8 LINKER SEQADV 6GH9 SER A 755 UNP Q9Y4E8 LINKER SEQADV 6GH9 LYS A 756 UNP Q9Y4E8 LINKER SEQADV 6GH9 ALA A 920 UNP Q9Y4E8 LYS 920 CONFLICT SEQADV 6GH9 ALA A 921 UNP Q9Y4E8 GLY 921 CONFLICT SEQADV 6GH9 LEU A 923 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 GLU A 924 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS A 925 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS A 926 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS A 927 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS A 928 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS A 929 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS A 930 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 MET B 254 UNP Q9Y4E8 INITIATING METHIONINE SEQADV 6GH9 ALA B 752 UNP Q9Y4E8 LINKER SEQADV 6GH9 SER B 753 UNP Q9Y4E8 LINKER SEQADV 6GH9 THR B 754 UNP Q9Y4E8 LINKER SEQADV 6GH9 SER B 755 UNP Q9Y4E8 LINKER SEQADV 6GH9 LYS B 756 UNP Q9Y4E8 LINKER SEQADV 6GH9 ALA B 920 UNP Q9Y4E8 LYS 920 CONFLICT SEQADV 6GH9 ALA B 921 UNP Q9Y4E8 GLY 921 CONFLICT SEQADV 6GH9 LEU B 923 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 GLU B 924 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS B 925 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS B 926 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS B 927 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS B 928 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS B 929 UNP Q9Y4E8 EXPRESSION TAG SEQADV 6GH9 HIS B 930 UNP Q9Y4E8 EXPRESSION TAG SEQRES 1 A 365 MET GLU GLN PRO GLY LEU CYS GLY LEU SER ASN LEU GLY SEQRES 2 A 365 ASN THR CYS PHE MET ASN SER ALA ILE GLN CYS LEU SER SEQRES 3 A 365 ASN THR PRO PRO LEU THR GLU TYR PHE LEU ASN ASP LYS SEQRES 4 A 365 TYR GLN GLU GLU LEU ASN PHE ASP ASN PRO LEU GLY MET SEQRES 5 A 365 ARG GLY GLU ILE ALA LYS SER TYR ALA GLU LEU ILE LYS SEQRES 6 A 365 GLN MET TRP SER GLY LYS PHE SER TYR VAL THR PRO ARG SEQRES 7 A 365 ALA PHE LYS THR GLN VAL GLY ARG PHE ALA PRO GLN PHE SEQRES 8 A 365 SER GLY TYR GLN GLN GLN ASP CYS GLN GLU LEU LEU ALA SEQRES 9 A 365 PHE LEU LEU ASP GLY LEU HIS GLU ASP LEU ASN ARG ILE SEQRES 10 A 365 ARG LYS LYS PRO TYR ILE GLN LEU LYS ASP ALA ASP GLY SEQRES 11 A 365 ARG PRO ASP LYS VAL VAL ALA GLU GLU ALA TRP GLU ASN SEQRES 12 A 365 HIS LEU LYS ARG ASN ASP SER ILE ILE VAL ASP ILE PHE SEQRES 13 A 365 HIS GLY LEU PHE LYS SER THR LEU VAL CYS PRO GLU CYS SEQRES 14 A 365 ALA LYS ILE SER VAL THR PHE ASP PRO PHE CYS TYR LEU SEQRES 15 A 365 THR LEU PRO LEU ALA SER THR SER LYS VAL LYS LEU LYS SEQRES 16 A 365 ASP CYS ILE GLU LEU PHE THR THR LYS GLU LYS LEU GLY SEQRES 17 A 365 ALA GLU ASP PRO TRP TYR CYS PRO ASN CYS LYS GLU HIS SEQRES 18 A 365 GLN GLN ALA THR LYS LYS LEU ASP LEU TRP SER LEU PRO SEQRES 19 A 365 PRO VAL LEU VAL VAL HIS LEU LYS ARG PHE SER TYR SER SEQRES 20 A 365 ARG TYR MET ARG ASP LYS LEU ASP THR LEU VAL ASP PHE SEQRES 21 A 365 PRO ILE ASN ASP LEU ASP MET SER GLU PHE LEU ILE ASN SEQRES 22 A 365 PRO ASN ALA GLY PRO CYS ARG TYR ASN LEU ILE ALA VAL SEQRES 23 A 365 SER ASN HIS TYR GLY GLY MET GLY GLY GLY HIS TYR THR SEQRES 24 A 365 ALA PHE ALA LYS ASN LYS ASP ASP GLY LYS TRP TYR TYR SEQRES 25 A 365 PHE ASP ASP SER SER VAL SER THR ALA SER GLU ASP GLN SEQRES 26 A 365 ILE VAL SER LYS ALA ALA TYR VAL LEU PHE TYR GLN ARG SEQRES 27 A 365 GLN ASP THR PHE SER GLY THR GLY PHE PHE PRO LEU ASP SEQRES 28 A 365 ARG GLU THR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS SEQRES 29 A 365 HIS SEQRES 1 B 365 MET GLU GLN PRO GLY LEU CYS GLY LEU SER ASN LEU GLY SEQRES 2 B 365 ASN THR CYS PHE MET ASN SER ALA ILE GLN CYS LEU SER SEQRES 3 B 365 ASN THR PRO PRO LEU THR GLU TYR PHE LEU ASN ASP LYS SEQRES 4 B 365 TYR GLN GLU GLU LEU ASN PHE ASP ASN PRO LEU GLY MET SEQRES 5 B 365 ARG GLY GLU ILE ALA LYS SER TYR ALA GLU LEU ILE LYS SEQRES 6 B 365 GLN MET TRP SER GLY LYS PHE SER TYR VAL THR PRO ARG SEQRES 7 B 365 ALA PHE LYS THR GLN VAL GLY ARG PHE ALA PRO GLN PHE SEQRES 8 B 365 SER GLY TYR GLN GLN GLN ASP CYS GLN GLU LEU LEU ALA SEQRES 9 B 365 PHE LEU LEU ASP GLY LEU HIS GLU ASP LEU ASN ARG ILE SEQRES 10 B 365 ARG LYS LYS PRO TYR ILE GLN LEU LYS ASP ALA ASP GLY SEQRES 11 B 365 ARG PRO ASP LYS VAL VAL ALA GLU GLU ALA TRP GLU ASN SEQRES 12 B 365 HIS LEU LYS ARG ASN ASP SER ILE ILE VAL ASP ILE PHE SEQRES 13 B 365 HIS GLY LEU PHE LYS SER THR LEU VAL CYS PRO GLU CYS SEQRES 14 B 365 ALA LYS ILE SER VAL THR PHE ASP PRO PHE CYS TYR LEU SEQRES 15 B 365 THR LEU PRO LEU ALA SER THR SER LYS VAL LYS LEU LYS SEQRES 16 B 365 ASP CYS ILE GLU LEU PHE THR THR LYS GLU LYS LEU GLY SEQRES 17 B 365 ALA GLU ASP PRO TRP TYR CYS PRO ASN CYS LYS GLU HIS SEQRES 18 B 365 GLN GLN ALA THR LYS LYS LEU ASP LEU TRP SER LEU PRO SEQRES 19 B 365 PRO VAL LEU VAL VAL HIS LEU LYS ARG PHE SER TYR SER SEQRES 20 B 365 ARG TYR MET ARG ASP LYS LEU ASP THR LEU VAL ASP PHE SEQRES 21 B 365 PRO ILE ASN ASP LEU ASP MET SER GLU PHE LEU ILE ASN SEQRES 22 B 365 PRO ASN ALA GLY PRO CYS ARG TYR ASN LEU ILE ALA VAL SEQRES 23 B 365 SER ASN HIS TYR GLY GLY MET GLY GLY GLY HIS TYR THR SEQRES 24 B 365 ALA PHE ALA LYS ASN LYS ASP ASP GLY LYS TRP TYR TYR SEQRES 25 B 365 PHE ASP ASP SER SER VAL SER THR ALA SER GLU ASP GLN SEQRES 26 B 365 ILE VAL SER LYS ALA ALA TYR VAL LEU PHE TYR GLN ARG SEQRES 27 B 365 GLN ASP THR PHE SER GLY THR GLY PHE PHE PRO LEU ASP SEQRES 28 B 365 ARG GLU THR ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS SEQRES 29 B 365 HIS HET ZN A1001 1 HET DMS A1002 4 HET MIX A1003 32 HETNAM ZN ZINC ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM MIX 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL) HETNAM 2 MIX AMINO]ETHYL}AMINO)-9,10-ANTHRACENEDIONE HETSYN MIX MITOXANTRONE; 1,4-DIHYDROXY-5,8-BIS({2-[(2- HETSYN 2 MIX HYDROXYETHYL)AMINO]ETHYL}AMINO)ANTHRA-9,10-QUINONE FORMUL 3 ZN ZN 2+ FORMUL 4 DMS C2 H6 O S FORMUL 5 MIX C22 H28 N4 O6 FORMUL 6 HOH *153(H2 O) HELIX 1 AA1 PHE A 270 ASN A 280 1 11 HELIX 2 AA2 THR A 281 ASN A 290 1 10 HELIX 3 AA3 TYR A 293 LEU A 297 5 5 HELIX 4 AA4 GLY A 307 TRP A 321 1 15 HELIX 5 AA5 PRO A 330 ALA A 341 1 12 HELIX 6 AA6 GLU A 354 LEU A 367 1 14 HELIX 7 AA7 PRO A 385 ASN A 401 1 17 HELIX 8 AA8 SER A 403 HIS A 410 1 8 HELIX 9 AA9 LEU A 759 THR A 767 1 9 HELIX 10 AB1 SER A 833 LEU A 836 5 4 HELIX 11 AB2 SER A 887 VAL A 892 1 6 HELIX 12 AB3 ASP A 905 PHE A 907 5 3 HELIX 13 AB4 PHE B 270 ASN B 280 1 11 HELIX 14 AB5 THR B 281 ASN B 290 1 10 HELIX 15 AB6 TYR B 293 LEU B 297 5 5 HELIX 16 AB7 GLY B 307 TRP B 321 1 15 HELIX 17 AB8 PRO B 330 ALA B 341 1 12 HELIX 18 AB9 GLU B 354 LEU B 367 1 14 HELIX 19 AC1 PRO B 385 ASN B 401 1 17 HELIX 20 AC2 SER B 403 HIS B 410 1 8 HELIX 21 AC3 LEU B 759 THR B 767 1 9 HELIX 22 AC4 SER B 887 ILE B 891 5 5 HELIX 23 AC5 ASP B 905 PHE B 907 5 3 SHEET 1 AA1 2 GLY A 261 LEU A 262 0 SHEET 2 AA1 2 TYR A 327 VAL A 328 1 O VAL A 328 N GLY A 261 SHEET 1 AA2 4 LYS A 424 PHE A 432 0 SHEET 2 AA2 4 GLY A 411 CYS A 419 -1 N CYS A 419 O LYS A 424 SHEET 3 AA2 4 THR A 790 SER A 797 -1 O ASP A 794 N LYS A 414 SHEET 4 AA2 4 GLU A 770 LYS A 771 -1 N GLU A 770 O LYS A 791 SHEET 1 AA3 5 LEU A 435 LEU A 437 0 SHEET 2 AA3 5 VAL A 801 LEU A 806 1 O VAL A 803 N LEU A 435 SHEET 3 AA3 5 ALA A 896 ARG A 903 -1 O LEU A 899 N VAL A 804 SHEET 4 AA3 5 ARG A 845 GLY A 857 -1 N ILE A 849 O PHE A 900 SHEET 5 AA3 5 LEU A 830 ASP A 831 -1 N LEU A 830 O TYR A 846 SHEET 1 AA4 7 LEU A 435 LEU A 437 0 SHEET 2 AA4 7 VAL A 801 LEU A 806 1 O VAL A 803 N LEU A 435 SHEET 3 AA4 7 ALA A 896 ARG A 903 -1 O LEU A 899 N VAL A 804 SHEET 4 AA4 7 ARG A 845 GLY A 857 -1 N ILE A 849 O PHE A 900 SHEET 5 AA4 7 GLY A 860 LYS A 868 -1 O THR A 864 N ASN A 853 SHEET 6 AA4 7 TRP A 875 ASP A 879 -1 O PHE A 878 N ALA A 865 SHEET 7 AA4 7 SER A 882 ALA A 886 -1 O SER A 884 N TYR A 877 SHEET 1 AA5 2 VAL A 757 LYS A 758 0 SHEET 2 AA5 2 VAL A 823 ASP A 824 1 O ASP A 824 N VAL A 757 SHEET 1 AA6 2 TRP A 778 CYS A 780 0 SHEET 2 AA6 2 GLU A 785 GLN A 787 -1 O GLU A 785 N CYS A 780 SHEET 1 AA7 2 GLY B 261 LEU B 262 0 SHEET 2 AA7 2 TYR B 327 VAL B 328 1 O VAL B 328 N GLY B 261 SHEET 1 AA8 3 LYS B 424 PHE B 432 0 SHEET 2 AA8 3 GLY B 411 CYS B 419 -1 N CYS B 419 O LYS B 424 SHEET 3 AA8 3 THR B 790 SER B 797 -1 O ASP B 794 N LYS B 414 SHEET 1 AA9 5 LEU B 435 LEU B 437 0 SHEET 2 AA9 5 VAL B 801 LEU B 806 1 O VAL B 803 N LEU B 435 SHEET 3 AA9 5 ALA B 896 ARG B 903 -1 O LEU B 899 N VAL B 804 SHEET 4 AA9 5 ARG B 845 HIS B 854 -1 N ILE B 849 O PHE B 900 SHEET 5 AA9 5 LEU B 830 ASP B 831 -1 N LEU B 830 O TYR B 846 SHEET 1 AB1 7 LEU B 435 LEU B 437 0 SHEET 2 AB1 7 VAL B 801 LEU B 806 1 O VAL B 803 N LEU B 435 SHEET 3 AB1 7 ALA B 896 ARG B 903 -1 O LEU B 899 N VAL B 804 SHEET 4 AB1 7 ARG B 845 HIS B 854 -1 N ILE B 849 O PHE B 900 SHEET 5 AB1 7 TYR B 863 LYS B 868 -1 O LYS B 868 N ILE B 849 SHEET 6 AB1 7 TRP B 875 ASP B 879 -1 O PHE B 878 N ALA B 865 SHEET 7 AB1 7 SER B 882 ALA B 886 -1 O SER B 884 N TYR B 877 SHEET 1 AB2 2 LYS B 756 LYS B 758 0 SHEET 2 AB2 2 LEU B 822 ASP B 824 1 O ASP B 824 N VAL B 757 LINK SG CYS A 419 ZN ZN A1001 1555 1555 2.39 LINK SG CYS A 422 ZN ZN A1001 1555 1555 2.28 LINK SG CYS A 780 ZN ZN A1001 1555 1555 2.52 LINK SG CYS A 783 ZN ZN A1001 1555 1555 2.51 SITE 1 AC1 4 CYS A 419 CYS A 422 CYS A 780 CYS A 783 SITE 1 AC2 2 ASP A 300 ARG A 371 SITE 1 AC3 5 ASN A 264 TYR A 855 GLY A 856 HIS A 862 SITE 2 AC3 5 ASP A 879 CRYST1 62.070 94.390 63.290 90.00 90.08 90.00 P 1 21 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 0.016111 0.000000 0.000022 0.00000 SCALE2 0.000000 0.010594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015800 0.00000