HEADER HYDROLASE 30-DEC-13 4O8Y TITLE ZINC-FREE RPN11 IN COMPLEX WITH RPN8 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 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: RPN8, YOR261C, O5360; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 559292; SOURCE 13 STRAIN: ATCC 204508 / S288C; SOURCE 14 GENE: RPN11, MPR1, YFR004W; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MPN JAMM, DEUBIQUITINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.J.WORDEN,C.PADOVANI,A.MARTIN REVDAT 5 20-SEP-23 4O8Y 1 REMARK SEQADV REVDAT 4 22-NOV-17 4O8Y 1 REMARK REVDAT 3 19-MAR-14 4O8Y 1 JRNL REVDAT 2 26-FEB-14 4O8Y 1 JRNL REVDAT 1 22-JAN-14 4O8Y 0 JRNL AUTH E.J.WORDEN,C.PADOVANI,A.MARTIN JRNL TITL STRUCTURE OF THE RPN11-RPN8 DIMER REVEALS MECHANISMS OF JRNL TITL 2 SUBSTRATE DEUBIQUITINATION DURING PROTEASOMAL DEGRADATION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 220 2014 JRNL REFN ISSN 1545-9993 JRNL PMID 24463465 JRNL DOI 10.1038/NSMB.2771 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 34734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.760 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 40.6233 - 4.6980 0.99 2741 167 0.1831 0.1952 REMARK 3 2 4.6980 - 3.7298 0.99 2581 159 0.1394 0.1858 REMARK 3 3 3.7298 - 3.2585 1.00 2555 156 0.1499 0.2033 REMARK 3 4 3.2585 - 2.9607 0.98 2467 151 0.1542 0.2165 REMARK 3 5 2.9607 - 2.7485 0.96 2420 146 0.1653 0.1945 REMARK 3 6 2.7485 - 2.5865 0.95 2394 147 0.1680 0.2738 REMARK 3 7 2.5865 - 2.4570 0.95 2371 145 0.1653 0.2225 REMARK 3 8 2.4570 - 2.3501 0.93 2304 140 0.1678 0.1945 REMARK 3 9 2.3501 - 2.2596 0.94 2346 144 0.1581 0.2185 REMARK 3 10 2.2596 - 2.1816 0.95 2347 144 0.1634 0.2184 REMARK 3 11 2.1816 - 2.1134 0.95 2369 144 0.1686 0.2220 REMARK 3 12 2.1134 - 2.0530 0.93 2307 141 0.1797 0.2026 REMARK 3 13 2.0530 - 1.9990 0.85 2077 127 0.1851 0.2795 REMARK 3 14 1.9990 - 1.9502 0.59 1455 89 0.1890 0.2198 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.85 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 : 0.013 2826 REMARK 3 ANGLE : 1.385 3779 REMARK 3 CHIRALITY : 0.062 429 REMARK 3 PLANARITY : 0.007 477 REMARK 3 DIHEDRAL : 16.884 1049 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4O8Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000084191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0750 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SAGITTAL FOCUSING MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.80700 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: PDB ENTRIES 4F70, 2O95 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG8000, 30% ETHYLENE GLYCOL, AND REMARK 280 100 MM HEPES (PH7.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 99.44350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.20250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.20250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 149.16525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.20250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.20250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.72175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.20250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.20250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 149.16525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.20250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.20250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.72175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 99.44350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 0 REMARK 465 GLY A 1 REMARK 465 LYS A 144 REMARK 465 ASP A 145 REMARK 465 ASP A 146 REMARK 465 GLY A 147 REMARK 465 THR A 148 REMARK 465 SER A 149 REMARK 465 LEU A 182 REMARK 465 PHE A 183 REMARK 465 GLN A 184 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 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 TRP B 221 REMARK 465 GLN B 222 REMARK 465 SER B 223 REMARK 465 GLY B 224 REMARK 465 LEU B 225 REMARK 465 LYS B 226 REMARK 465 MET B 227 REMARK 465 TYR B 228 REMARK 465 ASP B 229 REMARK 465 TYR B 230 REMARK 465 GLU B 231 REMARK 465 GLU B 232 REMARK 465 LYS B 233 REMARK 465 GLU B 234 REMARK 465 GLU B 235 REMARK 465 SER B 236 REMARK 465 ASN B 237 REMARK 465 LEU B 238 REMARK 465 ALA B 239 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 HIS B 204 CG ND1 CD2 CE1 NE2 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 O VAL B 147 H LYS B 150 1.59 REMARK 500 OE1 GLU A 29 O HOH A 434 2.10 REMARK 500 OE1 GLU B 48 O HOH B 513 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG B 135 O HOH A 420 5444 2.15 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 33 CB CYS A 33 SG -0.097 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 GLU A 29 -132.02 77.29 REMARK 500 GLU A 29 -179.23 -58.32 REMARK 500 ASN A 30 -8.74 13.43 REMARK 500 ASN A 62 101.93 -162.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 29 ASN A 30 -112.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4O8X RELATED DB: PDB REMARK 900 ZINC-BOUND RPN11 IN COMPLEX WITH RPN8 DBREF 4O8Y A 2 178 UNP Q08723 RPN8_YEAST 2 178 DBREF 4O8Y B 2 239 UNP P43588 RPN11_YEAST 2 239 SEQADV 4O8Y MET A 0 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y GLY A 1 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y LEU A 179 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y GLU A 180 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y VAL A 181 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y LEU A 182 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y PHE A 183 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y GLN A 184 UNP Q08723 EXPRESSION TAG SEQADV 4O8Y GLY B 0 UNP P43588 EXPRESSION TAG SEQADV 4O8Y PRO B 1 UNP P43588 EXPRESSION TAG SEQRES 1 A 185 MET GLY SER LEU GLN HIS GLU LYS VAL THR ILE ALA PRO SEQRES 2 A 185 LEU VAL LEU LEU SER ALA LEU ASP HIS TYR GLU ARG THR SEQRES 3 A 185 GLN THR LYS GLU ASN LYS ARG CYS VAL GLY VAL ILE LEU SEQRES 4 A 185 GLY ASP ALA ASN SER SER THR ILE ARG VAL THR ASN SER SEQRES 5 A 185 PHE ALA LEU PRO PHE GLU GLU ASP GLU LYS ASN SER ASP SEQRES 6 A 185 VAL TRP PHE LEU ASP HIS ASN TYR ILE GLU ASN MET ASN SEQRES 7 A 185 GLU MET CYS LYS LYS ILE ASN ALA LYS GLU LYS LEU ILE SEQRES 8 A 185 GLY TRP TYR HIS SER GLY PRO LYS LEU ARG ALA SER ASP SEQRES 9 A 185 LEU LYS ILE ASN GLU LEU PHE LYS LYS TYR THR GLN ASN SEQRES 10 A 185 ASN PRO LEU LEU LEU ILE VAL ASP VAL LYS GLN GLN GLY SEQRES 11 A 185 VAL GLY LEU PRO THR ASP ALA TYR VAL ALA ILE GLU GLN SEQRES 12 A 185 VAL LYS ASP ASP GLY THR SER THR GLU LYS THR PHE LEU SEQRES 13 A 185 HIS LEU PRO CYS THR ILE GLU ALA GLU GLU ALA GLU GLU SEQRES 14 A 185 ILE GLY VAL GLU HIS LEU LEU ARG ASP VAL LEU GLU VAL SEQRES 15 A 185 LEU PHE GLN SEQRES 1 B 240 GLY PRO GLU ARG LEU GLN ARG LEU MET MET ASN SER LYS SEQRES 2 B 240 VAL GLY SER ALA ASP THR GLY ARG ASP ASP THR LYS GLU SEQRES 3 B 240 THR VAL TYR ILE SER SER ILE ALA LEU LEU LYS MET LEU SEQRES 4 B 240 LYS HIS GLY ARG ALA GLY VAL PRO MET GLU VAL MET GLY SEQRES 5 B 240 LEU MET LEU GLY GLU PHE VAL ASP ASP TYR THR VAL ASN SEQRES 6 B 240 VAL VAL ASP VAL PHE ALA MET PRO GLN SER GLY THR GLY SEQRES 7 B 240 VAL SER VAL GLU ALA VAL ASP ASP VAL PHE GLN ALA LYS SEQRES 8 B 240 MET MET ASP MET LEU LYS GLN THR GLY ARG ASP GLN MET SEQRES 9 B 240 VAL VAL GLY TRP TYR HIS SER HIS PRO GLY PHE GLY CYS SEQRES 10 B 240 TRP LEU SER SER VAL ASP VAL ASN THR GLN LYS SER PHE SEQRES 11 B 240 GLU GLN LEU ASN SER ARG ALA VAL ALA VAL VAL VAL ASP SEQRES 12 B 240 PRO ILE GLN SER VAL LYS GLY LYS VAL VAL ILE ASP ALA SEQRES 13 B 240 PHE ARG LEU ILE ASP THR GLY ALA LEU ILE ASN ASN LEU SEQRES 14 B 240 GLU PRO ARG GLN THR THR SER ASN THR GLY LEU LEU ASN SEQRES 15 B 240 LYS ALA ASN ILE GLN ALA LEU ILE HIS GLY LEU ASN ARG SEQRES 16 B 240 HIS TYR TYR SER LEU ASN ILE ASP TYR HIS LYS THR ALA SEQRES 17 B 240 LYS GLU THR LYS MET LEU MET ASN LEU HIS LYS GLU GLN SEQRES 18 B 240 TRP GLN SER GLY LEU LYS MET TYR ASP TYR GLU GLU LYS SEQRES 19 B 240 GLU GLU SER ASN LEU ALA HET EDO A 201 10 HET EDO A 202 10 HET EDO A 203 10 HET EDO A 204 10 HET EDO A 205 10 HET EDO A 206 10 HET EDO A 207 10 HET EDO A 208 10 HET EDO A 209 10 HET EDO A 210 10 HET EDO A 211 10 HET EDO B 301 10 HET EDO B 302 10 HET EDO B 303 10 HET EDO B 304 10 HET EDO B 305 10 HET EDO B 306 10 HET EDO B 307 10 HET EDO B 308 10 HET EDO B 309 10 HET EDO B 310 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 21(C2 H6 O2) FORMUL 24 HOH *271(H2 O) HELIX 1 1 ALA A 11 THR A 25 1 15 HELIX 2 2 ASP A 69 ASN A 84 1 16 HELIX 3 3 SER A 102 LYS A 112 1 11 HELIX 4 4 GLU A 164 VAL A 181 1 18 HELIX 5 5 SER B 31 VAL B 45 1 15 HELIX 6 6 SER B 79 VAL B 83 5 5 HELIX 7 7 ASP B 84 GLN B 97 1 14 HELIX 8 8 SER B 119 ASN B 133 1 15 HELIX 9 9 THR B 206 MET B 214 1 9 SHEET 1 A 8 GLU A 151 LEU A 157 0 SHEET 2 A 8 THR A 134 GLN A 142 -1 N VAL A 138 O LEU A 155 SHEET 3 A 8 LEU A 119 VAL A 123 -1 N ILE A 122 O ASP A 135 SHEET 4 A 8 LYS A 88 HIS A 94 1 N TRP A 92 O LEU A 121 SHEET 5 A 8 VAL A 34 ASP A 40 -1 N GLY A 39 O LYS A 88 SHEET 6 A 8 THR A 45 ALA A 53 -1 O ARG A 47 N ASP A 40 SHEET 7 A 8 LYS A 7 ILE A 10 1 N THR A 9 O VAL A 48 SHEET 8 A 8 CYS A 159 ILE A 161 1 O THR A 160 N VAL A 8 SHEET 1 B 2 PHE A 56 ASP A 59 0 SHEET 2 B 2 ASN A 62 LEU A 68 -1 O PHE A 67 N GLU A 57 SHEET 1 C 8 TYR B 196 SER B 198 0 SHEET 2 C 8 ILE B 153 LEU B 158 -1 N ARG B 157 O TYR B 197 SHEET 3 C 8 VAL B 137 VAL B 141 -1 N ALA B 138 O PHE B 156 SHEET 4 C 8 MET B 103 SER B 110 1 N TRP B 107 O VAL B 139 SHEET 5 C 8 MET B 50 ASP B 59 -1 N GLY B 55 O MET B 103 SHEET 6 C 8 THR B 62 ALA B 70 -1 O ASP B 67 N LEU B 54 SHEET 7 C 8 THR B 26 SER B 30 1 N TYR B 28 O VAL B 65 SHEET 8 C 8 ASN B 200 HIS B 204 1 O ASN B 200 N VAL B 27 CISPEP 1 GLY A 96 PRO A 97 0 9.82 CISPEP 2 VAL B 45 PRO B 46 0 10.06 CISPEP 3 LYS B 148 GLY B 149 0 -17.06 SITE 1 AC1 3 ILE A 83 HIS B 40 ALA B 43 SITE 1 AC2 5 ASN A 50 EDO A 207 HOH A 366 HOH A 374 SITE 2 AC2 5 HOH B 476 SITE 1 AC3 3 LYS A 81 ILE A 83 ALA A 85 SITE 1 AC4 7 ARG A 100 ALA A 101 ASP A 103 LEU A 104 SITE 2 AC4 7 PHE A 154 HOH A 384 GLN B 145 SITE 1 AC5 5 PRO A 97 LYS A 98 LEU A 99 ASP A 135 SITE 2 AC5 5 TYR A 137 SITE 1 AC6 2 ASP A 64 TRP A 66 SITE 1 AC7 5 CYS A 80 ILE A 83 EDO A 202 HOH A 310 SITE 2 AC7 5 HOH A 334 SITE 1 AC8 6 ASP A 20 GLU A 23 HOH A 307 HOH A 365 SITE 2 AC8 6 GLU B 209 HOH B 409 SITE 1 AC9 2 GLU A 57 PHE A 67 SITE 1 BC1 7 TYR A 22 GLU A 29 LYS A 31 ARG A 32 SITE 2 BC1 7 SER A 95 GLY A 96 TRP B 117 SITE 1 BC2 5 GLU A 78 MET A 79 LYS A 82 HOH A 343 SITE 2 BC2 5 HOH B 483 SITE 1 BC3 3 VAL B 83 GLN B 88 LEU B 132 SITE 1 BC4 6 LYS A 98 ASP A 124 HOH A 423 HOH A 439 SITE 2 BC4 6 TYR B 196 HOH B 467 SITE 1 BC5 3 ILE B 153 HOH B 413 HOH B 470 SITE 1 BC6 2 SER B 198 ASN B 200 SITE 1 BC7 7 ALA A 166 ARG B 42 PRO B 143 SER B 146 SITE 2 BC7 7 HOH B 474 HOH B 475 HOH B 525 SITE 1 BC8 6 LYS A 112 THR A 114 HOH A 421 PHE B 57 SITE 2 BC8 6 VAL B 58 ARG B 135 SITE 1 BC9 6 GLU A 108 LYS A 111 ASN A 117 ALA A 139 SITE 2 BC9 6 LYS A 152 HOH A 406 SITE 1 CC1 7 PRO B 72 GLN B 73 SER B 74 VAL B 78 SITE 2 CC1 7 ALA B 82 HOH B 401 HOH B 459 SITE 1 CC2 2 MET B 214 HIS B 217 SITE 1 CC3 3 LYS B 96 GLY B 99 HOH B 482 CRYST1 70.405 70.405 198.887 90.00 90.00 90.00 P 43 21 2 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 0.014204 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005028 0.00000