HEADER SIGNALING PROTEIN/HYDROLASE 05-JUL-07 2QIY TITLE YEAST DEUBIQUITINASE UBP3 AND BRE5 COFACTOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBP3-ASSOCIATED PROTEIN BRE5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-146; COMPND 5 SYNONYM: BREFELDIN-A SENSITIVITY PROTEIN 5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 3; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: RESIDUES 190-233; COMPND 11 SYNONYM: UBIQUITIN THIOESTERASE 3, UBIQUITIN-SPECIFIC-PROCESSING COMPND 12 PROTEASE 3, DEUBIQUITINATING ENZYME 3; COMPND 13 EC: 3.1.2.15; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: BRE5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 GENE: UBP3; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS DEUBIQUITYLATION, UBIQUITIN-SPECIFIC PROCESSING PROTEASES(UBPS), KEYWDS 2 NTF2, PROTEIN-PROTEIN RECOGNITION, HYDROLASE, THIOL PROTEASE, UBL KEYWDS 3 CONJUGATION PATHWAY, PHOSPHORYLATION, RNA-BINDING, SIGNALING KEYWDS 4 PROTEIN-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.LI,X.LIU,R.MARMORSTEIN REVDAT 4 30-AUG-23 2QIY 1 SEQADV REVDAT 3 13-JUL-11 2QIY 1 VERSN REVDAT 2 24-FEB-09 2QIY 1 VERSN REVDAT 1 30-OCT-07 2QIY 0 JRNL AUTH K.LI,B.OSSAREH-NAZARI,X.LIU,C.DARGEMONT,R.MARMORSTEIN JRNL TITL MOLECULAR BASIS FOR BRE5 COFACTOR RECOGNITION BY THE UBP3 JRNL TITL 2 DEUBIQUITYLATING ENZYME. JRNL REF J.MOL.BIOL. V. 372 194 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17632125 JRNL DOI 10.1016/J.JMB.2007.06.052 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.LI,K.ZHAO,B.OSSAREH-NAZARI,G.DA,C.DARGEMONT,R.MARMORSTEIN REMARK 1 TITL STRUCTURAL BASIS FOR INTERACTION BETWEEN THE UBP3 REMARK 1 TITL 2 DEUBIQUTINATING ENZYME AND ITS BRE5 COFACTOR REMARK 1 REF J.BIOL.CHEM. V. 280 29176 2005 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15955808 REMARK 1 DOI 10.1074/JBC.M502975200 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 50599 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5681 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) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 286 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2580 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : -1.59000 REMARK 3 B33 (A**2) : 0.82000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.354 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2639 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3570 ; 1.469 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 309 ; 5.661 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;34.286 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 453 ;15.438 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.120 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 408 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1973 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1284 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1855 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 201 ; 0.124 ; 0.200 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): 23 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.235 ; 0.200 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): 1627 ; 0.870 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2575 ; 1.402 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1147 ; 2.241 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 995 ; 3.246 ; 4.500 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 : 4 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 3 A 143 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9880 22.0716 16.3398 REMARK 3 T TENSOR REMARK 3 T11: -0.0364 T22: -0.0380 REMARK 3 T33: -0.0590 T12: 0.0150 REMARK 3 T13: -0.0091 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.7455 L22: 1.7435 REMARK 3 L33: 1.0545 L12: 0.0350 REMARK 3 L13: -0.8565 L23: 0.1512 REMARK 3 S TENSOR REMARK 3 S11: -0.0201 S12: -0.1499 S13: -0.1274 REMARK 3 S21: 0.2305 S22: 0.0465 S23: -0.0538 REMARK 3 S31: 0.1023 S32: 0.1184 S33: -0.0264 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 : C 206 C 230 REMARK 3 ORIGIN FOR THE GROUP (A): 19.9798 20.3739 2.8462 REMARK 3 T TENSOR REMARK 3 T11: -0.1039 T22: -0.0373 REMARK 3 T33: 0.0016 T12: 0.0156 REMARK 3 T13: 0.0035 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 2.4721 L22: 0.7026 REMARK 3 L33: 5.6990 L12: -0.3286 REMARK 3 L13: -1.1608 L23: -0.8196 REMARK 3 S TENSOR REMARK 3 S11: -0.1564 S12: 0.0319 S13: -0.0724 REMARK 3 S21: -0.0401 S22: -0.0802 S23: -0.2416 REMARK 3 S31: -0.0234 S32: 0.2166 S33: 0.2366 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 : B 4 B 145 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0711 44.3847 16.4141 REMARK 3 T TENSOR REMARK 3 T11: -0.0315 T22: -0.0884 REMARK 3 T33: -0.0206 T12: -0.0094 REMARK 3 T13: 0.0813 T23: -0.0405 REMARK 3 L TENSOR REMARK 3 L11: 1.0409 L22: 2.6997 REMARK 3 L33: 1.7301 L12: 0.4559 REMARK 3 L13: -0.2941 L23: 0.6277 REMARK 3 S TENSOR REMARK 3 S11: 0.1084 S12: -0.0589 S13: 0.2731 REMARK 3 S21: 0.0096 S22: 0.0855 S23: 0.0236 REMARK 3 S31: -0.2757 S32: 0.0580 S33: -0.1939 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 : D 206 D 230 REMARK 3 ORIGIN FOR THE GROUP (A): 14.9576 45.6305 -1.3435 REMARK 3 T TENSOR REMARK 3 T11: 0.0883 T22: -0.1288 REMARK 3 T33: -0.0871 T12: -0.0656 REMARK 3 T13: 0.1570 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 7.1123 L22: 2.0213 REMARK 3 L33: 4.5550 L12: 0.6737 REMARK 3 L13: -1.3078 L23: 0.8430 REMARK 3 S TENSOR REMARK 3 S11: 0.1788 S12: 0.6488 S13: 0.2045 REMARK 3 S21: -0.7258 S22: 0.1826 S23: -0.2209 REMARK 3 S31: -0.4839 S32: 0.2002 S33: -0.3614 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2QIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9176 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50599 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 49.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB 1ZX2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%(W/V) PEG 20000, 100MM BICINE, 2% REMARK 280 DIOXAN, PH 9.0, EVAPORATION, TEMPERATURE 293K 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 29.55000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.74000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.12000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.74000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.55000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.12000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6190 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D 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 -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 46 REMARK 465 THR A 47 REMARK 465 ASN A 48 REMARK 465 GLU A 49 REMARK 465 SER A 126 REMARK 465 ASN A 127 REMARK 465 GLY A 128 REMARK 465 SER A 144 REMARK 465 PHE A 145 REMARK 465 LYS A 146 REMARK 465 LEU A 147 REMARK 465 GLU A 148 REMARK 465 GLY C 186 REMARK 465 SER C 187 REMARK 465 ALA C 188 REMARK 465 SER C 189 REMARK 465 VAL C 190 REMARK 465 THR C 191 REMARK 465 LYS C 192 REMARK 465 LEU C 193 REMARK 465 LYS C 194 REMARK 465 ASN C 195 REMARK 465 LEU C 196 REMARK 465 LYS C 197 REMARK 465 GLU C 198 REMARK 465 ASN C 199 REMARK 465 SER C 200 REMARK 465 SER C 201 REMARK 465 ASN C 202 REMARK 465 LEU C 203 REMARK 465 ILE C 204 REMARK 465 GLN C 205 REMARK 465 ALA C 231 REMARK 465 LEU C 232 REMARK 465 ASN C 233 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 HIS B -3 REMARK 465 MET B -2 REMARK 465 ALA B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 VAL B 3 REMARK 465 LYS B 45 REMARK 465 SER B 46 REMARK 465 THR B 47 REMARK 465 ASN B 48 REMARK 465 GLU B 49 REMARK 465 LYS B 50 REMARK 465 SER B 126 REMARK 465 ASN B 127 REMARK 465 GLY B 128 REMARK 465 LYS B 146 REMARK 465 LEU B 147 REMARK 465 GLU B 148 REMARK 465 GLY D 186 REMARK 465 SER D 187 REMARK 465 ALA D 188 REMARK 465 SER D 189 REMARK 465 VAL D 190 REMARK 465 THR D 191 REMARK 465 LYS D 192 REMARK 465 LEU D 193 REMARK 465 LYS D 194 REMARK 465 ASN D 195 REMARK 465 LEU D 196 REMARK 465 LYS D 197 REMARK 465 GLU D 198 REMARK 465 ASN D 199 REMARK 465 SER D 200 REMARK 465 SER D 201 REMARK 465 ASN D 202 REMARK 465 LEU D 203 REMARK 465 ILE D 204 REMARK 465 GLN D 205 REMARK 465 ALA D 231 REMARK 465 LEU D 232 REMARK 465 ASN D 233 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 71 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 71 CG CD NE CZ NH1 NH2 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 OE2 GLU A 36 NE2 HIS B 95 2.06 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 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -6.0 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 ASP A 23 88.97 -166.81 REMARK 500 ASP B 23 91.94 -163.53 REMARK 500 GLU D 214 -52.48 133.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZX2 RELATED DB: PDB REMARK 900 BRE5 UNIT OF THE BRE5/UBP3 COMPLEX DBREF 2QIY A 1 146 UNP P53741 BRE5_YEAST 1 146 DBREF 2QIY C 190 233 UNP Q01477 UBP3_YEAST 190 233 DBREF 2QIY B 1 146 UNP P53741 BRE5_YEAST 1 146 DBREF 2QIY D 190 233 UNP Q01477 UBP3_YEAST 190 233 SEQADV 2QIY GLY A -5 UNP P53741 EXPRESSION TAG SEQADV 2QIY SER A -4 UNP P53741 EXPRESSION TAG SEQADV 2QIY HIS A -3 UNP P53741 EXPRESSION TAG SEQADV 2QIY MET A -2 UNP P53741 EXPRESSION TAG SEQADV 2QIY ALA A -1 UNP P53741 EXPRESSION TAG SEQADV 2QIY SER A 0 UNP P53741 EXPRESSION TAG SEQADV 2QIY LEU A 147 UNP P53741 EXPRESSION TAG SEQADV 2QIY GLU A 148 UNP P53741 EXPRESSION TAG SEQADV 2QIY GLY C 186 UNP Q01477 EXPRESSION TAG SEQADV 2QIY SER C 187 UNP Q01477 EXPRESSION TAG SEQADV 2QIY ALA C 188 UNP Q01477 EXPRESSION TAG SEQADV 2QIY SER C 189 UNP Q01477 EXPRESSION TAG SEQADV 2QIY GLY B -5 UNP P53741 EXPRESSION TAG SEQADV 2QIY SER B -4 UNP P53741 EXPRESSION TAG SEQADV 2QIY HIS B -3 UNP P53741 EXPRESSION TAG SEQADV 2QIY MET B -2 UNP P53741 EXPRESSION TAG SEQADV 2QIY ALA B -1 UNP P53741 EXPRESSION TAG SEQADV 2QIY SER B 0 UNP P53741 EXPRESSION TAG SEQADV 2QIY LEU B 147 UNP P53741 EXPRESSION TAG SEQADV 2QIY GLU B 148 UNP P53741 EXPRESSION TAG SEQADV 2QIY GLY D 186 UNP Q01477 EXPRESSION TAG SEQADV 2QIY SER D 187 UNP Q01477 EXPRESSION TAG SEQADV 2QIY ALA D 188 UNP Q01477 EXPRESSION TAG SEQADV 2QIY SER D 189 UNP Q01477 EXPRESSION TAG SEQRES 1 A 154 GLY SER HIS MET ALA SER MET GLY VAL THR VAL GLN ASP SEQRES 2 A 154 ILE CYS PHE ALA PHE LEU GLN ASN TYR TYR GLU ARG MET SEQRES 3 A 154 ARG THR ASP PRO SER LYS LEU ALA TYR PHE TYR ALA SER SEQRES 4 A 154 THR ALA GLU LEU THR HIS THR ASN TYR GLN SER LYS SER SEQRES 5 A 154 THR ASN GLU LYS ASP ASP VAL LEU PRO THR VAL LYS VAL SEQRES 6 A 154 THR GLY ARG GLU ASN ILE ASN LYS PHE PHE SER ARG ASN SEQRES 7 A 154 ASP ALA LYS VAL ARG SER LEU LYS LEU LYS LEU ASP THR SEQRES 8 A 154 ILE ASP PHE GLN TYR THR GLY HIS LEU HIS LYS SER ILE SEQRES 9 A 154 LEU ILE MET ALA THR GLY GLU MET PHE TRP THR GLY THR SEQRES 10 A 154 PRO VAL TYR LYS PHE CYS GLN THR PHE ILE LEU LEU PRO SEQRES 11 A 154 SER SER ASN GLY SER THR PHE ASP ILE THR ASN ASP ILE SEQRES 12 A 154 ILE ARG PHE ILE SER ASN SER PHE LYS LEU GLU SEQRES 1 C 48 GLY SER ALA SER VAL THR LYS LEU LYS ASN LEU LYS GLU SEQRES 2 C 48 ASN SER SER ASN LEU ILE GLN LEU PRO LEU PHE ILE ASN SEQRES 3 C 48 THR THR GLU ALA GLU PHE ALA ALA ALA SER VAL GLN ARG SEQRES 4 C 48 TYR GLU LEU ASN MET LYS ALA LEU ASN SEQRES 1 B 154 GLY SER HIS MET ALA SER MET GLY VAL THR VAL GLN ASP SEQRES 2 B 154 ILE CYS PHE ALA PHE LEU GLN ASN TYR TYR GLU ARG MET SEQRES 3 B 154 ARG THR ASP PRO SER LYS LEU ALA TYR PHE TYR ALA SER SEQRES 4 B 154 THR ALA GLU LEU THR HIS THR ASN TYR GLN SER LYS SER SEQRES 5 B 154 THR ASN GLU LYS ASP ASP VAL LEU PRO THR VAL LYS VAL SEQRES 6 B 154 THR GLY ARG GLU ASN ILE ASN LYS PHE PHE SER ARG ASN SEQRES 7 B 154 ASP ALA LYS VAL ARG SER LEU LYS LEU LYS LEU ASP THR SEQRES 8 B 154 ILE ASP PHE GLN TYR THR GLY HIS LEU HIS LYS SER ILE SEQRES 9 B 154 LEU ILE MET ALA THR GLY GLU MET PHE TRP THR GLY THR SEQRES 10 B 154 PRO VAL TYR LYS PHE CYS GLN THR PHE ILE LEU LEU PRO SEQRES 11 B 154 SER SER ASN GLY SER THR PHE ASP ILE THR ASN ASP ILE SEQRES 12 B 154 ILE ARG PHE ILE SER ASN SER PHE LYS LEU GLU SEQRES 1 D 48 GLY SER ALA SER VAL THR LYS LEU LYS ASN LEU LYS GLU SEQRES 2 D 48 ASN SER SER ASN LEU ILE GLN LEU PRO LEU PHE ILE ASN SEQRES 3 D 48 THR THR GLU ALA GLU PHE ALA ALA ALA SER VAL GLN ARG SEQRES 4 D 48 TYR GLU LEU ASN MET LYS ALA LEU ASN FORMUL 5 HOH *220(H2 O) HELIX 1 1 THR A 4 ASP A 23 1 20 HELIX 2 2 PRO A 24 TYR A 29 5 6 HELIX 3 3 GLY A 61 ASN A 72 1 12 HELIX 4 4 ASN A 72 ARG A 77 1 6 HELIX 5 5 GLY A 92 LYS A 96 5 5 HELIX 6 6 THR C 213 MET C 229 1 17 HELIX 7 7 THR B 4 ASP B 23 1 20 HELIX 8 8 LYS B 26 TYR B 29 5 4 HELIX 9 9 GLY B 61 ASN B 72 1 12 HELIX 10 10 ASN B 72 SER B 78 1 7 HELIX 11 11 GLY B 92 LYS B 96 5 5 HELIX 12 12 GLU D 214 MET D 229 1 16 SHEET 1 A 7 THR A 56 THR A 60 0 SHEET 2 A 7 TYR A 31 THR A 40 -1 N LEU A 37 O VAL A 59 SHEET 3 A 7 PHE A 131 ILE A 141 1 O ASP A 136 N THR A 38 SHEET 4 A 7 TYR A 114 PRO A 124 -1 N ILE A 121 O THR A 134 SHEET 5 A 7 SER A 97 TRP A 108 -1 N MET A 106 O TYR A 114 SHEET 6 A 7 LEU A 79 THR A 91 -1 N GLN A 89 O LEU A 99 SHEET 7 A 7 LEU C 208 ILE C 210 -1 O LEU C 208 N LEU A 83 SHEET 1 B 7 THR B 56 THR B 60 0 SHEET 2 B 7 TYR B 31 THR B 40 -1 N LEU B 37 O VAL B 59 SHEET 3 B 7 PHE B 131 ILE B 141 1 O ILE B 133 N ALA B 32 SHEET 4 B 7 TYR B 114 PRO B 124 -1 N LEU B 123 O ASP B 132 SHEET 5 B 7 SER B 97 TRP B 108 -1 N MET B 106 O TYR B 114 SHEET 6 B 7 LEU B 79 THR B 91 -1 N LYS B 80 O PHE B 107 SHEET 7 B 7 LEU D 208 ILE D 210 -1 O LEU D 208 N LEU B 83 CISPEP 1 LEU C 206 PRO C 207 0 0.36 CISPEP 2 LEU D 206 PRO D 207 0 -7.03 CRYST1 59.100 90.240 101.480 90.00 90.00 90.00 P 21 21 21 8 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 0.016920 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009854 0.00000