HEADER PROTEIN BINDING 05-DEC-16 5U4P TITLE PROTEIN-PROTEIN COMPLEX BETWEEN 26S PROTEASOME REGULATORY SUBUNIT TITLE 2 RPN8, RPN11, AND UBIQUITIN S31 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN8; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN11; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE RPN11,PROTEIN MPR1; COMPND 9 EC: 3.4.19.12; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: UBIQUITIN-40S RIBOSOMAL PROTEIN S31; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: RPN8, YOR261C, O5360; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 12 S288C); SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 559292; SOURCE 15 STRAIN: ATCC 204508 / S288C; SOURCE 16 GENE: RPN11, MPR1, YFR004W; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 21 S288C); SOURCE 22 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 23 ORGANISM_TAXID: 559292; SOURCE 24 STRAIN: ATCC 204508 / S288C; SOURCE 25 GENE: RPS31, RPS37, UBI3, YLR167W, L9470.14; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, UBIQUITIN, PROTEASOME, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR E.J.WORDEN,K.C.DONG,A.MARTIN REVDAT 5 04-OCT-23 5U4P 1 LINK REVDAT 4 01-JAN-20 5U4P 1 REMARK REVDAT 3 27-SEP-17 5U4P 1 REMARK REVDAT 2 20-SEP-17 5U4P 1 JRNL REVDAT 1 06-SEP-17 5U4P 0 JRNL AUTH E.J.WORDEN,K.C.DONG,A.MARTIN JRNL TITL AN AAA MOTOR-DRIVEN MECHANICAL SWITCH IN RPN11 CONTROLS JRNL TITL 2 DEUBIQUITINATION AT THE 26S PROTEASOME. JRNL REF MOL. CELL V. 67 799 2017 JRNL REFN ISSN 1097-4164 JRNL PMID 28844860 JRNL DOI 10.1016/J.MOLCEL.2017.07.023 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 109.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 23100 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 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 : 1156 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.015 3307 REMARK 3 ANGLE : 1.198 4460 REMARK 3 CHIRALITY : 0.060 516 REMARK 3 PLANARITY : 0.007 568 REMARK 3 DIHEDRAL : 17.197 1232 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -3.9943 -49.7135 18.8511 REMARK 3 T TENSOR REMARK 3 T11: 0.4750 T22: 0.3200 REMARK 3 T33: 0.4695 T12: -0.0712 REMARK 3 T13: 0.1394 T23: -0.0642 REMARK 3 L TENSOR REMARK 3 L11: 4.0329 L22: 5.5024 REMARK 3 L33: 6.5122 L12: 1.3532 REMARK 3 L13: -1.3825 L23: -2.7365 REMARK 3 S TENSOR REMARK 3 S11: -0.0875 S12: -0.0831 S13: -0.1034 REMARK 3 S21: -0.2251 S22: 0.0329 S23: -0.2780 REMARK 3 S31: 0.7704 S32: -0.1313 S33: 0.0624 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 1.9680 -31.9797 -0.5931 REMARK 3 T TENSOR REMARK 3 T11: 0.4556 T22: 0.5547 REMARK 3 T33: 0.6697 T12: -0.0035 REMARK 3 T13: 0.1539 T23: 0.1948 REMARK 3 L TENSOR REMARK 3 L11: 4.4361 L22: 5.2574 REMARK 3 L33: 7.4635 L12: 1.5802 REMARK 3 L13: -1.9191 L23: -2.4439 REMARK 3 S TENSOR REMARK 3 S11: -0.2053 S12: 0.9122 S13: 0.7779 REMARK 3 S21: -0.4805 S22: 0.1251 S23: 0.0639 REMARK 3 S31: 0.3717 S32: -0.3528 S33: 0.0255 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -0.0595 -47.7716 -20.9391 REMARK 3 T TENSOR REMARK 3 T11: 1.9743 T22: 1.9484 REMARK 3 T33: 0.7471 T12: -0.5687 REMARK 3 T13: 0.3501 T23: -0.1407 REMARK 3 L TENSOR REMARK 3 L11: 1.8880 L22: 2.6913 REMARK 3 L33: 3.6210 L12: -1.1629 REMARK 3 L13: 1.3705 L23: 1.3407 REMARK 3 S TENSOR REMARK 3 S11: -0.3175 S12: 1.9714 S13: -0.6268 REMARK 3 S21: -1.5276 S22: 0.0308 S23: -0.4781 REMARK 3 S31: 1.5640 S32: -0.5501 S33: 0.3280 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 5U4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1159 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23105 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 109.301 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : 0.08667 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 109.3 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, RMSM, 4UN2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM TARTRATE, PH 6.8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.24667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.62333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.93500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.31167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.55833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 93.24667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 46.62333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 23.31167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 69.93500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 116.55833 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -175.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.93500 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 A 226 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 GLY B 0 REMARK 465 PRO B 1 REMARK 465 GLU B 2 REMARK 465 ARG B 3 REMARK 465 LEU B 4 REMARK 465 GLN B 5 REMARK 465 ARG B 6 REMARK 465 LEU B 7 REMARK 465 MET B 8 REMARK 465 MET B 9 REMARK 465 ASN B 10 REMARK 465 SER B 11 REMARK 465 LYS B 12 REMARK 465 VAL B 13 REMARK 465 GLY B 14 REMARK 465 SER B 15 REMARK 465 ALA B 16 REMARK 465 ASP B 17 REMARK 465 THR B 18 REMARK 465 GLY B 19 REMARK 465 ARG B 20 REMARK 465 ASP B 21 REMARK 465 ASP B 22 REMARK 465 THR B 23 REMARK 465 ASP B 160 REMARK 465 THR B 161 REMARK 465 GLY B 162 REMARK 465 ALA B 163 REMARK 465 LEU B 164 REMARK 465 ILE B 165 REMARK 465 ASN B 166 REMARK 465 ASN B 167 REMARK 465 LEU B 168 REMARK 465 GLU B 169 REMARK 465 PRO B 170 REMARK 465 ARG B 171 REMARK 465 GLN B 172 REMARK 465 THR B 173 REMARK 465 THR B 174 REMARK 465 SER B 175 REMARK 465 ASN B 176 REMARK 465 THR B 177 REMARK 465 GLY B 178 REMARK 465 LEU B 179 REMARK 465 LEU B 180 REMARK 465 ASN B 181 REMARK 465 LYS B 182 REMARK 465 ALA B 183 REMARK 465 ASN B 184 REMARK 465 ILE B 185 REMARK 465 GLN B 186 REMARK 465 ALA B 187 REMARK 465 LEU B 188 REMARK 465 ILE B 189 REMARK 465 HIS B 190 REMARK 465 GLY B 191 REMARK 465 LEU B 192 REMARK 465 ASN B 193 REMARK 465 LYS B 205 REMARK 465 LYS B 218 REMARK 465 GLU B 219 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 B 194 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 74 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 HD22 ASN B 133 O HOH B 401 1.23 REMARK 500 O LYS A 28 H LYS A 31 1.58 REMARK 500 O THR B 206 HG1 THR B 210 1.58 REMARK 500 O HOH A 217 O HOH A 232 1.91 REMARK 500 ND2 ASN B 133 O HOH B 401 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 159 CB CYS A 159 SG -0.114 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 PRO A 133 33.14 -85.11 REMARK 500 ASP A 145 70.71 -67.66 REMARK 500 VAL B 78 23.97 -140.00 REMARK 500 PRO B 112 94.51 -61.64 REMARK 500 ASN B 133 105.10 -164.25 REMARK 500 HIS B 195 174.90 -55.66 REMARK 500 SER C 19 -6.81 -59.60 REMARK 500 SER C 20 70.72 -101.28 REMARK 500 REMARK 500 REMARK: NULL 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 B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 109 NE2 REMARK 620 2 HIS B 111 NE2 107.4 REMARK 620 3 ASP B 122 OD2 86.5 160.9 REMARK 620 4 GLY C 76 O 108.7 94.2 93.7 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 B 301 DBREF 5U4P A 1 177 UNP Q08723 RPN8_YEAST 1 177 DBREF 5U4P B 2 219 UNP P43588 RPN11_YEAST 2 219 DBREF 5U4P C 1 76 UNP P05759 RS27A_YEAST 1 76 SEQADV 5U4P GLY B 0 UNP P43588 EXPRESSION TAG SEQADV 5U4P PRO B 1 UNP P43588 EXPRESSION TAG SEQRES 1 A 177 MET SER LEU GLN HIS GLU LYS VAL THR ILE ALA PRO LEU SEQRES 2 A 177 VAL LEU LEU SER ALA LEU ASP HIS TYR GLU ARG THR GLN SEQRES 3 A 177 THR LYS GLU ASN LYS ARG CYS VAL GLY VAL ILE LEU GLY SEQRES 4 A 177 ASP ALA ASN SER SER THR ILE ARG VAL THR ASN SER PHE SEQRES 5 A 177 ALA LEU PRO PHE GLU GLU ASP GLU LYS ASN SER ASP VAL SEQRES 6 A 177 TRP PHE LEU ASP HIS ASN TYR ILE GLU ASN MET ASN GLU SEQRES 7 A 177 MET CYS LYS LYS ILE ASN ALA LYS GLU LYS LEU ILE GLY SEQRES 8 A 177 TRP TYR HIS SER GLY PRO LYS LEU ARG ALA SER ASP LEU SEQRES 9 A 177 LYS ILE ASN GLU LEU PHE LYS LYS TYR THR GLN ASN ASN SEQRES 10 A 177 PRO LEU LEU LEU ILE VAL ASP VAL LYS GLN GLN GLY VAL SEQRES 11 A 177 GLY LEU PRO THR ASP ALA TYR VAL ALA ILE GLU GLN VAL SEQRES 12 A 177 LYS ASP ASP GLY THR SER THR GLU LYS THR PHE LEU HIS SEQRES 13 A 177 LEU PRO CYS THR ILE GLU ALA GLU GLU ALA GLU GLU ILE SEQRES 14 A 177 GLY VAL GLU HIS LEU LEU ARG ASP SEQRES 1 B 220 GLY PRO GLU ARG LEU GLN ARG LEU MET MET ASN SER LYS SEQRES 2 B 220 VAL GLY SER ALA ASP THR GLY ARG ASP ASP THR LYS GLU SEQRES 3 B 220 THR VAL TYR ILE SER SER ILE ALA LEU LEU LYS MET LEU SEQRES 4 B 220 LYS HIS GLY ARG ALA GLY VAL PRO MET GLU VAL MET GLY SEQRES 5 B 220 LEU MET LEU GLY GLU PHE VAL ASP ASP TYR THR VAL ASN SEQRES 6 B 220 VAL VAL ASP VAL PHE ALA MET PRO GLN SER GLY THR GLY SEQRES 7 B 220 VAL SER VAL GLU ALA VAL ASP ASP VAL PHE GLN ALA LYS SEQRES 8 B 220 MET MET ASP MET LEU LYS GLN THR GLY ARG ASP GLN MET SEQRES 9 B 220 VAL VAL GLY TRP TYR HIS SER HIS PRO GLY PHE GLY CYS SEQRES 10 B 220 TRP LEU SER SER VAL ASP VAL ASN THR GLN LYS SER PHE SEQRES 11 B 220 GLU GLN LEU ASN SER ARG ALA VAL ALA VAL VAL VAL ASP SEQRES 12 B 220 PRO ILE GLN SER VAL LYS GLY LYS VAL VAL ILE ASP ALA SEQRES 13 B 220 PHE ARG LEU ILE ASP THR GLY ALA LEU ILE ASN ASN LEU SEQRES 14 B 220 GLU PRO ARG GLN THR THR SER ASN THR GLY LEU LEU ASN SEQRES 15 B 220 LYS ALA ASN ILE GLN ALA LEU ILE HIS GLY LEU ASN ARG SEQRES 16 B 220 HIS TYR TYR SER LEU ASN ILE ASP TYR HIS LYS THR ALA SEQRES 17 B 220 LYS GLU THR LYS MET LEU MET ASN LEU HIS LYS GLU SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU SER SER ASP THR ILE ASP ASN VAL SEQRES 3 C 76 LYS SER LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN B 301 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *63(H2 O) HELIX 1 AA1 ALA A 11 THR A 25 1 15 HELIX 2 AA2 ASP A 69 ASN A 84 1 16 HELIX 3 AA3 SER A 102 LYS A 111 1 10 HELIX 4 AA4 GLU A 164 LEU A 175 1 12 HELIX 5 AA5 SER B 30 VAL B 45 1 16 HELIX 6 AA6 ASP B 85 THR B 98 1 14 HELIX 7 AA7 SER B 119 ASN B 133 1 15 HELIX 8 AA8 ALA B 207 MET B 214 1 8 HELIX 9 AA9 THR C 22 GLY C 35 1 14 HELIX 10 AB1 PRO C 37 ASP C 39 5 3 HELIX 11 AB2 THR C 55 ASN C 60 1 6 SHEET 1 AA1 8 THR A 150 LEU A 157 0 SHEET 2 AA1 8 THR A 134 VAL A 143 -1 N VAL A 138 O LEU A 155 SHEET 3 AA1 8 LEU A 119 VAL A 123 -1 N LEU A 120 O TYR A 137 SHEET 4 AA1 8 LYS A 88 HIS A 94 1 N TRP A 92 O LEU A 121 SHEET 5 AA1 8 VAL A 34 ASP A 40 -1 N GLY A 35 O TYR A 93 SHEET 6 AA1 8 THR A 45 ALA A 53 -1 O PHE A 52 N VAL A 36 SHEET 7 AA1 8 LYS A 7 ILE A 10 1 N THR A 9 O VAL A 48 SHEET 8 AA1 8 CYS A 159 ILE A 161 1 O THR A 160 N ILE A 10 SHEET 1 AA2 2 PHE A 56 GLU A 58 0 SHEET 2 AA2 2 TRP A 66 LEU A 68 -1 O PHE A 67 N GLU A 57 SHEET 1 AA3 8 THR B 26 ILE B 29 0 SHEET 2 AA3 8 THR B 62 PHE B 69 1 O VAL B 63 N TYR B 28 SHEET 3 AA3 8 MET B 50 ASP B 59 -1 N LEU B 54 O ASP B 67 SHEET 4 AA3 8 MET B 103 SER B 110 -1 O TYR B 108 N GLY B 51 SHEET 5 AA3 8 VAL B 137 VAL B 141 1 O VAL B 139 N TRP B 107 SHEET 6 AA3 8 ILE B 153 LEU B 158 -1 O PHE B 156 N ALA B 138 SHEET 7 AA3 8 TYR B 196 ASP B 202 -1 O LEU B 199 N ALA B 155 SHEET 8 AA3 8 THR B 26 ILE B 29 1 N VAL B 27 O ASN B 200 SHEET 1 AA4 3 GLN B 73 THR B 76 0 SHEET 2 AA4 3 SER B 79 ALA B 82 -1 O SER B 79 N THR B 76 SHEET 3 AA4 3 ARG C 74 GLY C 75 -1 O GLY C 75 N VAL B 80 SHEET 1 AA5 5 THR C 12 GLU C 16 0 SHEET 2 AA5 5 GLN C 2 THR C 7 -1 N ILE C 3 O LEU C 15 SHEET 3 AA5 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4 SHEET 4 AA5 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 AA5 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK NE2 HIS B 109 ZN ZN B 301 1555 1555 2.27 LINK NE2 HIS B 111 ZN ZN B 301 1555 1555 1.94 LINK OD2 ASP B 122 ZN ZN B 301 1555 1555 1.93 LINK ZN ZN B 301 O GLY C 76 1555 1555 2.04 CISPEP 1 GLY A 96 PRO A 97 0 3.64 CISPEP 2 ASP A 146 GLY A 147 0 8.19 CISPEP 3 VAL B 45 PRO B 46 0 9.16 SITE 1 AC1 4 HIS B 109 HIS B 111 ASP B 122 GLY C 76 CRYST1 126.210 126.210 139.870 90.00 90.00 120.00 P 65 2 2 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 0.007923 0.004575 0.000000 0.00000 SCALE2 0.000000 0.009149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007149 0.00000