PDB Short entry for 4UEL HEADER HYDROLASE 18-DEC-14 4UEL TITLE UCH-L5 IN COMPLEX WITH UBIQUITIN-PROPARGYL BOUND TO THE RPN13 DEUBAD TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UCH-L5, UBIQUITIN C-TERMINAL HYDROLASE UCH37, UBIQUITIN COMPND 5 THIOESTERASE L5; COMPND 6 EC: 3.4.19.12; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: ACTIVE SITE CYS88 COVALENTLY LINKED TO UBIQUITIN- COMPND 9 PROPARGYL; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: POLYUBIQUITIN-B; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: UBIQUITIN; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 OTHER_DETAILS: GLY76 OF UBIQUITIN IS REPLACED BY GLY-AYE THAT IS COMPND 17 COVALENTLY LINKED TO THE ACTIVE SITE CYS88 OF UCH-L5; COMPND 18 MOL_ID: 3; COMPND 19 MOLECULE: PROTEASOMAL UBIQUITIN RECEPTOR ADRM1; COMPND 20 CHAIN: C; COMPND 21 FRAGMENT: DEUBAD DOMAIN, RESIDUES 266-388; COMPND 22 SYNONYM: RPN13,110 KDA CELL MEMBRANE GLYCOPROTEIN, GP110, ADHESION- COMPND 23 REGULATING MOLECULE 1, ARM-1, PROTEASOME REGULATORY PARTICLE NON- COMPND 24 ATPASE 13, HRPN13, RPN13 HOMOLOG; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 VARIANT: ISOFORM 3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-NKI-3C-LIC; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 23 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 24 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2; SOURCE 25 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 26 EXPRESSION_SYSTEM_PLASMID: PCDF-NKI-HIS-3C-LIC KEYWDS HYDROLASE, DEUBIQUITINATING ENZYME, DUB, UCH37, UCHL5, PROTEASOME, KEYWDS 2 ADRM1, RPN13, DEUBAD, UCH, UBIQUITIN-PROPARGYL EXPDTA X-RAY DIFFRACTION AUTHOR D.D.SAHTOE,W.J.VAN DIJK,F.EL OUALID,R.EKKEBUS,H.OVAA,T.K.SIXMA REVDAT 3 03-APR-19 4UEL 1 REMARK LINK REVDAT 2 25-MAR-15 4UEL 1 JRNL REVDAT 1 04-MAR-15 4UEL 0 JRNL AUTH D.D.SAHTOE,W.J.VAN DIJK,F.EL OUALID,R.EKKEBUS,H.OVAA, JRNL AUTH 2 T.K.SIXMA JRNL TITL MECHANISM OF UCH-L5 ACTIVATION AND INHIBITION BY DEUBAD JRNL TITL 2 DOMAINS IN RPN13 AND INO80G. JRNL REF MOL.CELL V. 57 887 2015 JRNL REFN ISSN 1097-2765 JRNL PMID 25702870 JRNL DOI 10.1016/J.MOLCEL.2014.12.039 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25531 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1354 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1827 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3762 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.65000 REMARK 3 B22 (A**2) : -0.63000 REMARK 3 B33 (A**2) : -2.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.185 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.370 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3830 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3717 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5169 ; 0.993 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8570 ; 0.683 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 472 ; 5.084 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;38.060 ;25.668 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 706 ;13.323 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.080 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 578 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4350 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 849 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1897 ; 2.932 ; 1.877 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1896 ; 2.933 ; 1.877 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2363 ; 4.278 ; 2.799 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1933 ; 4.021 ; 2.273 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 228 REMARK 3 ORIGIN FOR THE GROUP (A): -0.1700 97.4860 30.2110 REMARK 3 T TENSOR REMARK 3 T11: 0.1306 T22: 0.0793 REMARK 3 T33: 0.0229 T12: 0.0252 REMARK 3 T13: -0.0007 T23: -0.0182 REMARK 3 L TENSOR REMARK 3 L11: 1.3230 L22: 1.4534 REMARK 3 L33: 1.4525 L12: -0.3286 REMARK 3 L13: -0.5495 L23: 0.3445 REMARK 3 S TENSOR REMARK 3 S11: -0.0639 S12: -0.0564 S13: 0.0045 REMARK 3 S21: -0.0298 S22: 0.0338 S23: -0.0396 REMARK 3 S31: 0.1174 S32: 0.0702 S33: 0.0301 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 229 A 315 REMARK 3 ORIGIN FOR THE GROUP (A): 4.1750 89.9760 6.6730 REMARK 3 T TENSOR REMARK 3 T11: 0.3732 T22: 0.2614 REMARK 3 T33: 0.0664 T12: 0.0026 REMARK 3 T13: -0.0176 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 3.7160 L22: 6.4542 REMARK 3 L33: 1.2248 L12: -3.6527 REMARK 3 L13: 1.9919 L23: -2.5644 REMARK 3 S TENSOR REMARK 3 S11: -0.0045 S12: 0.1630 S13: 0.0947 REMARK 3 S21: 0.0251 S22: -0.1083 S23: -0.2318 REMARK 3 S31: -0.0776 S32: 0.0811 S33: 0.1127 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 316 A 320 REMARK 3 ORIGIN FOR THE GROUP (A): 36.3110 78.6350 14.8550 REMARK 3 T TENSOR REMARK 3 T11: 0.9239 T22: 0.7959 REMARK 3 T33: 1.1441 T12: -0.0741 REMARK 3 T13: 0.1773 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 5.0140 L22: 2.7039 REMARK 3 L33: 2.1472 L12: -3.6447 REMARK 3 L13: 3.2168 L23: -2.3703 REMARK 3 S TENSOR REMARK 3 S11: 0.2635 S12: 0.5891 S13: -0.3876 REMARK 3 S21: -0.0772 S22: -0.2784 S23: 0.2348 REMARK 3 S31: 0.0673 S32: 0.3989 S33: 0.0149 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 75 REMARK 3 ORIGIN FOR THE GROUP (A): 19.8180 97.3460 11.9730 REMARK 3 T TENSOR REMARK 3 T11: 0.1585 T22: 0.1096 REMARK 3 T33: 0.1023 T12: -0.0072 REMARK 3 T13: 0.0316 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 2.2142 L22: 2.5717 REMARK 3 L33: 3.6940 L12: 0.1824 REMARK 3 L13: -1.2345 L23: -0.8970 REMARK 3 S TENSOR REMARK 3 S11: 0.0318 S12: 0.0181 S13: 0.1706 REMARK 3 S21: -0.2648 S22: 0.0368 S23: -0.2127 REMARK 3 S31: -0.0290 S32: 0.3038 S33: -0.0685 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 287 C 307 REMARK 3 ORIGIN FOR THE GROUP (A): 23.5020 73.5720 7.0550 REMARK 3 T TENSOR REMARK 3 T11: 0.6208 T22: 0.5308 REMARK 3 T33: 0.7619 T12: -0.0574 REMARK 3 T13: 0.0606 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 10.3175 L22: 0.4522 REMARK 3 L33: 5.2650 L12: 1.7329 REMARK 3 L13: 0.8509 L23: -0.7369 REMARK 3 S TENSOR REMARK 3 S11: -0.0507 S12: -0.0457 S13: 0.9937 REMARK 3 S21: 0.0265 S22: -0.2630 S23: 0.0574 REMARK 3 S31: -0.2733 S32: 1.3812 S33: 0.3137 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 308 C 363 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0980 71.7320 14.7480 REMARK 3 T TENSOR REMARK 3 T11: 0.0714 T22: 0.0936 REMARK 3 T33: 0.0871 T12: -0.0156 REMARK 3 T13: 0.0319 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 1.6690 L22: 5.6850 REMARK 3 L33: 2.4423 L12: 0.1524 REMARK 3 L13: 0.7421 L23: -0.8717 REMARK 3 S TENSOR REMARK 3 S11: 0.1204 S12: 0.0208 S13: -0.0228 REMARK 3 S21: -0.1824 S22: -0.1262 S23: -0.3610 REMARK 3 S31: -0.0552 S32: 0.0319 S33: 0.0058 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 364 C 384 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9080 62.1870 20.6650 REMARK 3 T TENSOR REMARK 3 T11: 0.4375 T22: 0.3764 REMARK 3 T33: 1.1623 T12: -0.0037 REMARK 3 T13: -0.4456 T23: 0.2261 REMARK 3 L TENSOR REMARK 3 L11: 9.9702 L22: 0.2668 REMARK 3 L33: 16.5324 L12: -0.5523 REMARK 3 L13: -6.8067 L23: 0.7993 REMARK 3 S TENSOR REMARK 3 S11: -0.4380 S12: 0.1272 S13: 0.2899 REMARK 3 S21: 0.2606 S22: -0.0954 S23: -0.4708 REMARK 3 S31: 0.3704 S32: 0.4360 S33: 0.5335 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4UEL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062585. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.83000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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: NULL REMARK 200 REMARK 200 REMARK: MOLECULAR REPLACEMENT WAS PERFORMED WITH THE PARTIALLY REMARK 200 BUILD UCH-L5-RPN13 STRUCTURE, SEE RELATED PDB REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS-PROPANE PH 5.8, 300 MM REMARK 280 NABR, 21% PEG3350. 4 DEGREES CELSIUS, 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 29.67000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.10550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.10550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.67000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.30000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -2 REMARK 465 PRO A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLY A 3 REMARK 465 ASN A 4 REMARK 465 ALA A 5 REMARK 465 LYS A 154 REMARK 465 THR A 155 REMARK 465 SER A 156 REMARK 465 ALA A 157 REMARK 465 LYS A 158 REMARK 465 GLU A 159 REMARK 465 PRO A 246 REMARK 465 MET A 247 REMARK 465 ASP A 248 REMARK 465 THR A 249 REMARK 465 ASP A 250 REMARK 465 GLN A 251 REMARK 465 GLY A 252 REMARK 465 ALA A 321 REMARK 465 LYS A 322 REMARK 465 LYS A 323 REMARK 465 ALA A 324 REMARK 465 GLN A 325 REMARK 465 GLU A 326 REMARK 465 THR A 327 REMARK 465 LYS A 328 REMARK 465 GLY C 262 REMARK 465 PRO C 263 REMARK 465 GLY C 264 REMARK 465 SER C 265 REMARK 465 ASP C 266 REMARK 465 LEU C 267 REMARK 465 GLN C 268 REMARK 465 SER C 269 REMARK 465 ILE C 270 REMARK 465 LEU C 271 REMARK 465 ALA C 272 REMARK 465 THR C 273 REMARK 465 MET C 274 REMARK 465 ASN C 275 REMARK 465 VAL C 276 REMARK 465 PRO C 277 REMARK 465 ALA C 278 REMARK 465 GLY C 279 REMARK 465 PRO C 280 REMARK 465 ALA C 281 REMARK 465 GLY C 282 REMARK 465 GLY C 283 REMARK 465 GLN C 284 REMARK 465 GLN C 285 REMARK 465 VAL C 286 REMARK 465 ALA C 385 REMARK 465 LYS C 386 REMARK 465 PRO C 387 REMARK 465 GLU C 388 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 GLU A 7 -63.79 -97.18 REMARK 500 MET A 148 -57.34 64.80 REMARK 500 ASP A 195 75.29 -161.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UEM RELATED DB: PDB REMARK 900 UCH-L5 IN COMPLEX WITH THE RPN13 DEUBAD DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 GLY76 IN NATIVE UBIQUITIN IS REPLACED BY AYE DBREF 4UEL A 1 328 UNP Q9Y5K5 UCHL5_HUMAN 1 328 DBREF 4UEL B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 4UEL C 266 388 UNP Q16186 ADRM1_HUMAN 266 388 SEQADV 4UEL GLY A -2 UNP Q9Y5K5 EXPRESSION TAG SEQADV 4UEL PRO A -1 UNP Q9Y5K5 EXPRESSION TAG SEQADV 4UEL GLY A 0 UNP Q9Y5K5 EXPRESSION TAG SEQADV 4UEL AYE B 76 UNP P0CG47 GLY 76 ENGINEERED MUTATION SEQADV 4UEL GLY C 262 UNP Q16186 EXPRESSION TAG SEQADV 4UEL PRO C 263 UNP Q16186 EXPRESSION TAG SEQADV 4UEL GLY C 264 UNP Q16186 EXPRESSION TAG SEQADV 4UEL SER C 265 UNP Q16186 EXPRESSION TAG SEQRES 1 A 331 GLY PRO GLY MET THR GLY ASN ALA GLY GLU TRP CYS LEU SEQRES 2 A 331 MET GLU SER ASP PRO GLY VAL PHE THR GLU LEU ILE LYS SEQRES 3 A 331 GLY PHE GLY CYS ARG GLY ALA GLN VAL GLU GLU ILE TRP SEQRES 4 A 331 SER LEU GLU PRO GLU ASN PHE GLU LYS LEU LYS PRO VAL SEQRES 5 A 331 HIS GLY LEU ILE PHE LEU PHE LYS TRP GLN PRO GLY GLU SEQRES 6 A 331 GLU PRO ALA GLY SER VAL VAL GLN ASP SER ARG LEU ASP SEQRES 7 A 331 THR ILE PHE PHE ALA LYS GLN VAL ILE ASN ASN ALA CYS SEQRES 8 A 331 ALA THR GLN ALA ILE VAL SER VAL LEU LEU ASN CYS THR SEQRES 9 A 331 HIS GLN ASP VAL HIS LEU GLY GLU THR LEU SER GLU PHE SEQRES 10 A 331 LYS GLU PHE SER GLN SER PHE ASP ALA ALA MET LYS GLY SEQRES 11 A 331 LEU ALA LEU SER ASN SER ASP VAL ILE ARG GLN VAL HIS SEQRES 12 A 331 ASN SER PHE ALA ARG GLN GLN MET PHE GLU PHE ASP THR SEQRES 13 A 331 LYS THR SER ALA LYS GLU GLU ASP ALA PHE HIS PHE VAL SEQRES 14 A 331 SER TYR VAL PRO VAL ASN GLY ARG LEU TYR GLU LEU ASP SEQRES 15 A 331 GLY LEU ARG GLU GLY PRO ILE ASP LEU GLY ALA CYS ASN SEQRES 16 A 331 GLN ASP ASP TRP ILE SER ALA VAL ARG PRO VAL ILE GLU SEQRES 17 A 331 LYS ARG ILE GLN LYS TYR SER GLU GLY GLU ILE ARG PHE SEQRES 18 A 331 ASN LEU MET ALA ILE VAL SER ASP ARG LYS MET ILE TYR SEQRES 19 A 331 GLU GLN LYS ILE ALA GLU LEU GLN ARG GLN LEU ALA GLU SEQRES 20 A 331 GLU PRO MET ASP THR ASP GLN GLY ASN SER MET LEU SER SEQRES 21 A 331 ALA ILE GLN SER GLU VAL ALA LYS ASN GLN MET LEU ILE SEQRES 22 A 331 GLU GLU GLU VAL GLN LYS LEU LYS ARG TYR LYS ILE GLU SEQRES 23 A 331 ASN ILE ARG ARG LYS HIS ASN TYR LEU PRO PHE ILE MET SEQRES 24 A 331 GLU LEU LEU LYS THR LEU ALA GLU HIS GLN GLN LEU ILE SEQRES 25 A 331 PRO LEU VAL GLU LYS ALA LYS GLU LYS GLN ASN ALA LYS SEQRES 26 A 331 LYS ALA GLN GLU THR LYS SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY AYE SEQRES 1 C 127 GLY PRO GLY SER ASP LEU GLN SER ILE LEU ALA THR MET SEQRES 2 C 127 ASN VAL PRO ALA GLY PRO ALA GLY GLY GLN GLN VAL ASP SEQRES 3 C 127 LEU ALA SER VAL LEU THR PRO GLU ILE MET ALA PRO ILE SEQRES 4 C 127 LEU ALA ASN ALA ASP VAL GLN GLU ARG LEU LEU PRO TYR SEQRES 5 C 127 LEU PRO SER GLY GLU SER LEU PRO GLN THR ALA ASP GLU SEQRES 6 C 127 ILE GLN ASN THR LEU THR SER PRO GLN PHE GLN GLN ALA SEQRES 7 C 127 LEU GLY MET PHE SER ALA ALA LEU ALA SER GLY GLN LEU SEQRES 8 C 127 GLY PRO LEU MET CYS GLN PHE GLY LEU PRO ALA GLU ALA SEQRES 9 C 127 VAL GLU ALA ALA ASN LYS GLY ASP VAL GLU ALA PHE ALA SEQRES 10 C 127 LYS ALA MET GLN ASN ASN ALA LYS PRO GLU HET AYE B 76 4 HETNAM AYE PROP-2-EN-1-AMINE HETSYN AYE ALLYLAMINE FORMUL 2 AYE C3 H7 N FORMUL 4 HOH *234(H2 O) HELIX 1 1 ASP A 14 GLY A 26 1 13 HELIX 2 2 PRO A 40 LYS A 45 1 6 HELIX 3 3 ASP A 71 THR A 76 5 6 HELIX 4 4 ALA A 87 LEU A 98 1 12 HELIX 5 5 LEU A 107 GLN A 119 1 13 HELIX 6 6 ASP A 122 ASN A 132 1 11 HELIX 7 7 SER A 133 SER A 142 1 10 HELIX 8 8 TRP A 196 LYS A 210 1 15 HELIX 9 9 ASP A 226 GLU A 245 1 20 HELIX 10 10 ASN A 253 HIS A 289 1 37 HELIX 11 11 TYR A 291 HIS A 305 1 15 HELIX 12 12 GLN A 307 LYS A 318 1 12 HELIX 13 13 THR B 22 GLY B 35 1 14 HELIX 14 14 PRO B 37 ASP B 39 5 3 HELIX 15 15 LEU B 56 ASN B 60 5 5 HELIX 16 16 ASP C 287 LEU C 292 1 6 HELIX 17 17 PRO C 294 ILE C 296 5 3 HELIX 18 18 MET C 297 ALA C 302 1 6 HELIX 19 19 ASN C 303 LEU C 311 1 9 HELIX 20 20 PRO C 312 LEU C 314 5 3 HELIX 21 21 THR C 323 ASP C 325 5 3 HELIX 22 22 GLU C 326 THR C 332 1 7 HELIX 23 23 SER C 333 SER C 349 1 17 HELIX 24 24 LEU C 352 PHE C 359 1 8 HELIX 25 25 PRO C 362 GLY C 372 1 11 HELIX 26 26 ASP C 373 ASN C 384 1 12 SHEET 1 AA 2 MET A 11 GLU A 12 0 SHEET 2 AA 2 ARG B 74 GLY B 75 -1 O GLY B 75 N MET A 11 SHEET 1 AB 7 ALA A 30 ILE A 35 0 SHEET 2 AB 7 ASN A 219 SER A 225 -1 O LEU A 220 N ILE A 35 SHEET 3 AB 7 VAL A 49 LYS A 57 -1 N HIS A 50 O ILE A 223 SHEET 4 AB 7 PHE A 163 VAL A 171 -1 O HIS A 164 N PHE A 56 SHEET 5 AB 7 ARG A 174 LEU A 178 -1 O ARG A 174 N VAL A 171 SHEET 6 AB 7 ILE A 186 ALA A 190 -1 O ILE A 186 N GLU A 177 SHEET 7 AB 7 SER A 67 VAL A 68 -1 O SER A 67 N ASP A 187 SHEET 1 BA 5 THR B 12 GLU B 16 0 SHEET 2 BA 5 GLN B 2 LYS B 6 -1 O ILE B 3 N LEU B 15 SHEET 3 BA 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 BA 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70 SHEET 5 BA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK C GLY B 75 N1 AYE B 76 1555 1555 1.33 LINK C2 AYE B 76 SG CYS A 88 1555 1555 1.68 CISPEP 1 LYS A 47 PRO A 48 0 2.84 CRYST1 59.340 98.600 100.211 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 0.016852 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010142 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009979 0.00000