HEADER HYDROLASE 27-APR-14 4Q8H TITLE STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2 PSEUDOUBIQUITIN- TITLE 2 HYDROLASE-RNASE MODULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 460-1115; COMPND 5 SYNONYM: PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN DEADENYLATION COMPLEX COMPND 6 CATALYTIC SUBUNIT 2; COMPND 7 EC: 3.1.13.4; 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: 4932; SOURCE 5 GENE: PAN2, YGL094C; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFL KEYWDS UBIQUITIN CARBOXYL-TERMINAL HYDROLASE-LIKE DOMAIN, UCH, RNASE, PAN3, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.B.SCHAEFER,E.CONTI REVDAT 4 20-SEP-23 4Q8H 1 REMARK SEQADV LINK REVDAT 3 16-JUL-14 4Q8H 1 JRNL REVDAT 2 02-JUL-14 4Q8H 1 JRNL REVDAT 1 04-JUN-14 4Q8H 0 JRNL AUTH I.B.SCHAFER,M.RODE,F.BONNEAU,S.SCHUSSLER,E.CONTI JRNL TITL THE STRUCTURE OF THE PAN2-PAN3 CORE COMPLEX REVEALS JRNL TITL 2 CROSS-TALK BETWEEN DEADENYLASE AND PSEUDOKINASE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 591 2014 JRNL REFN ISSN 1545-9993 JRNL PMID 24880344 JRNL DOI 10.1038/NSMB.2834 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1647) 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 25241 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1268 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 48.0185 - 6.4437 1.00 2817 144 0.2097 0.2442 REMARK 3 2 6.4437 - 5.1164 1.00 2695 149 0.2464 0.2801 REMARK 3 3 5.1164 - 4.4702 1.00 2672 152 0.1973 0.2488 REMARK 3 4 4.4702 - 4.0617 1.00 2649 154 0.2161 0.2505 REMARK 3 5 4.0617 - 3.7707 1.00 2639 143 0.2494 0.2883 REMARK 3 6 3.7707 - 3.5485 1.00 2621 139 0.2910 0.3275 REMARK 3 7 3.5485 - 3.3708 1.00 2651 123 0.3027 0.3127 REMARK 3 8 3.3708 - 3.2241 1.00 2630 134 0.3435 0.3857 REMARK 3 9 3.2241 - 3.1000 0.99 2599 130 0.4038 0.4483 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) : 0.530 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.00 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 : 0.004 5013 REMARK 3 ANGLE : 0.872 6803 REMARK 3 CHIRALITY : 0.035 772 REMARK 3 PLANARITY : 0.003 877 REMARK 3 DIHEDRAL : 12.329 1802 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 459 THROUGH 499 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9955 54.0065 54.8437 REMARK 3 T TENSOR REMARK 3 T11: 1.5774 T22: 1.4140 REMARK 3 T33: 0.8402 T12: 0.1529 REMARK 3 T13: -0.0372 T23: 0.1296 REMARK 3 L TENSOR REMARK 3 L11: 7.2656 L22: 2.3555 REMARK 3 L33: 5.3590 L12: -2.2911 REMARK 3 L13: -2.0860 L23: 3.2905 REMARK 3 S TENSOR REMARK 3 S11: -0.3197 S12: -1.3513 S13: -0.0536 REMARK 3 S21: 1.7036 S22: 0.8584 S23: -0.0690 REMARK 3 S31: -0.1011 S32: 0.1022 S33: -0.3454 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 500 THROUGH 618 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9402 67.3976 37.2028 REMARK 3 T TENSOR REMARK 3 T11: 0.6100 T22: 0.7073 REMARK 3 T33: 0.5088 T12: 0.0020 REMARK 3 T13: -0.0110 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 5.1079 L22: 7.0398 REMARK 3 L33: 7.6444 L12: 0.5249 REMARK 3 L13: 0.3866 L23: 0.2035 REMARK 3 S TENSOR REMARK 3 S11: -0.2675 S12: -0.4742 S13: 0.1187 REMARK 3 S21: 0.1151 S22: 0.2004 S23: 0.4306 REMARK 3 S31: -0.3619 S32: -0.5145 S33: 0.1124 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 619 THROUGH 881 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6930 57.4683 25.8206 REMARK 3 T TENSOR REMARK 3 T11: 0.5142 T22: 0.9905 REMARK 3 T33: 0.4824 T12: 0.1365 REMARK 3 T13: -0.0091 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 2.9658 L22: 3.7409 REMARK 3 L33: 4.3553 L12: 0.1611 REMARK 3 L13: 0.4502 L23: 0.1516 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: 0.6864 S13: -0.2449 REMARK 3 S21: -0.4691 S22: 0.0328 S23: -0.1239 REMARK 3 S31: -0.0220 S32: 0.4092 S33: -0.0629 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 882 THROUGH 1111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7690 86.1129 55.7775 REMARK 3 T TENSOR REMARK 3 T11: 0.8362 T22: 0.5526 REMARK 3 T33: 0.7710 T12: 0.0779 REMARK 3 T13: 0.1141 T23: -0.1098 REMARK 3 L TENSOR REMARK 3 L11: 3.0248 L22: 4.3917 REMARK 3 L33: 5.0410 L12: 0.4286 REMARK 3 L13: 0.2085 L23: 2.3792 REMARK 3 S TENSOR REMARK 3 S11: 0.0496 S12: -0.1031 S13: 0.0909 REMARK 3 S21: 0.4523 S22: -0.3634 S23: 0.8313 REMARK 3 S31: -0.2678 S32: -0.6961 S33: 0.2247 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 4Q8H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085736. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939080 REMARK 200 MONOCHROMATOR : CHANNEL CUT SI(111) 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25287 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.013 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 2.48800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: PDB ENTRIES 1WLJ AND 4Q8G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE, PH 5.5, 10% V/V REMARK 280 PEG200, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.85600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.75250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 128.72450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.85600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.75250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 128.72450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.85600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.75250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 128.72450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.85600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.75250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 128.72450 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 SG CYS A 716 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 A 458 REMARK 465 LEU A 583 REMARK 465 GLU A 584 REMARK 465 ASN A 585 REMARK 465 GLY A 586 REMARK 465 GLU A 587 REMARK 465 PRO A 588 REMARK 465 GLN A 589 REMARK 465 GLU A 590 REMARK 465 HIS A 591 REMARK 465 LEU A 592 REMARK 465 VAL A 682 REMARK 465 ILE A 683 REMARK 465 LYS A 684 REMARK 465 GLN A 685 REMARK 465 LEU A 686 REMARK 465 ASN A 687 REMARK 465 LYS A 688 REMARK 465 LYS A 689 REMARK 465 SER A 690 REMARK 465 ASN A 691 REMARK 465 GLN A 926 REMARK 465 GLY A 927 REMARK 465 ILE A 928 REMARK 465 ARG A 929 REMARK 465 SER A 930 REMARK 465 ILE A 931 REMARK 465 THR A 1112 REMARK 465 SER A 1113 REMARK 465 LYS A 1114 REMARK 465 GLY A 1115 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 SER A 486 OG REMARK 470 ARG A 488 CG CD NE CZ NH1 NH2 REMARK 470 THR A 491 OG1 CG2 REMARK 470 ASP A 492 CG OD1 OD2 REMARK 470 LYS A 580 CG CD CE NZ REMARK 470 GLN A 582 CG CD OE1 NE2 REMARK 470 GLU A 593 CG CD OE1 OE2 REMARK 470 TYR A 595 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 605 CG1 CG2 CD1 REMARK 470 GLU A 606 CG CD OE1 OE2 REMARK 470 ASN A 609 CG OD1 ND2 REMARK 470 LYS A 615 CG CD CE NZ REMARK 470 ILE A 678 CG1 CG2 CD1 REMARK 470 LYS A 680 CG CD CE NZ REMARK 470 SER A 711 OG REMARK 470 ILE A 712 CG1 CG2 CD1 REMARK 470 LYS A 718 CG CD CE NZ REMARK 470 THR A 719 OG1 CG2 REMARK 470 GLU A 720 CG CD OE1 OE2 REMARK 470 ASN A 882 CG OD1 ND2 REMARK 470 ARG A 885 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 886 CG OD1 OD2 REMARK 470 ARG A 889 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 890 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 891 CG CD OE1 OE2 REMARK 470 LEU A 920 CG CD1 CD2 REMARK 470 HIS A 925 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 932 CG1 CG2 CD1 REMARK 470 ARG A 933 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 964 CG OD1 ND2 REMARK 470 ASN A 966 CG OD1 ND2 REMARK 470 LEU A 972 CG CD1 CD2 REMARK 470 ARG A 974 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 979 CG CD1 CD2 REMARK 470 LEU A 983 CG CD1 CD2 REMARK 470 GLU A 986 CG CD OE1 OE2 REMARK 470 LYS A 987 CG CD CE NZ REMARK 470 LYS A 990 CG CD CE NZ REMARK 470 ASN A 996 CG OD1 ND2 REMARK 470 VAL A 997 CG1 CG2 REMARK 470 ILE A1038 CG1 CG2 CD1 REMARK 470 LYS A1044 CG CD CE NZ REMARK 470 TYR A1054 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A1057 CG CD1 CD2 REMARK 470 MET A1059 CG SD CE REMARK 470 ASN A1060 CG OD1 ND2 REMARK 470 ILE A1061 CG1 CG2 CD1 REMARK 470 GLN A1062 CG CD OE1 NE2 REMARK 470 GLU A1063 CG CD OE1 OE2 REMARK 470 ASN A1065 CG OD1 ND2 REMARK 470 LYS A1086 CG CD CE NZ REMARK 470 GLU A1087 CD OE1 OE2 REMARK 470 LEU A1095 CG CD1 CD2 REMARK 470 LYS A1108 CG CD CE NZ REMARK 470 VAL A1109 CG1 CG2 REMARK 470 GLU A1111 CG CD OE1 OE2 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 MG MG A 1201 MG MG A 1202 1.29 REMARK 500 OH TYR A 523 OD1 ASN A 623 2.05 REMARK 500 O ASP A 982 NH1 ARG A 991 2.06 REMARK 500 OG1 THR A 887 O SER A 988 2.12 REMARK 500 O PRO A 732 OH TYR A 787 2.17 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 CB CYS A 716 SG CYS A 716 3555 1.79 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 HIS A 514 -53.59 64.30 REMARK 500 LYS A 580 43.91 -75.67 REMARK 500 PHE A 608 -122.25 33.19 REMARK 500 SER A 611 -121.83 52.72 REMARK 500 ASN A 679 -100.09 53.29 REMARK 500 LYS A 766 -121.90 58.51 REMARK 500 LEU A 778 118.59 -166.55 REMARK 500 THR A 781 -55.90 -124.88 REMARK 500 ASP A 826 -110.27 56.39 REMARK 500 ARG A 889 176.16 60.76 REMARK 500 GLU A 891 107.49 -58.78 REMARK 500 SER A 918 65.01 -156.80 REMARK 500 GLU A 919 176.53 60.51 REMARK 500 GLU A 922 -65.51 71.85 REMARK 500 GLU A 949 98.05 -63.88 REMARK 500 ASP A 959 83.93 -153.67 REMARK 500 SER A 988 -60.34 67.25 REMARK 500 THR A 989 -159.94 -153.34 REMARK 500 ARG A 994 30.34 -90.33 REMARK 500 ARG A 995 63.95 -116.01 REMARK 500 ARG A1034 64.30 67.15 REMARK 500 ARG A1103 -39.02 -38.65 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 MG A1201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 910 OD1 REMARK 620 2 ASP A 910 OD2 61.9 REMARK 620 3 GLU A 912 OE2 99.5 87.7 REMARK 620 4 ASP A1071 OD2 129.9 86.6 118.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 910 OD2 REMARK 620 2 GLU A 912 OE2 93.4 REMARK 620 3 ASP A1071 OD2 106.0 159.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q8G RELATED DB: PDB REMARK 900 STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2 PSEUDOUBIQUITIN- REMARK 900 HYDROLASE REMARK 900 RELATED ID: 4Q8J RELATED DB: PDB REMARK 900 STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2-PAN3 CORE COMPLEX DBREF 4Q8H A 460 1115 UNP P53010 PAN2_YEAST 460 1115 SEQADV 4Q8H GLY A 458 UNP P53010 EXPRESSION TAG SEQADV 4Q8H PRO A 459 UNP P53010 EXPRESSION TAG SEQRES 1 A 658 GLY PRO GLU THR SER ASP ILE GLN THR TYR THR SER ILE SEQRES 2 A 658 ASN LYS TYR GLU VAL PRO PRO ALA TYR SER ARG LEU PRO SEQRES 3 A 658 LEU THR SER GLY ARG PHE GLY THR ASP ASN PHE ASP PHE SEQRES 4 A 658 THR PRO PHE ASN ASN THR GLU TYR SER GLY LEU ASP PRO SEQRES 5 A 658 ASP VAL ASP ASN HIS TYR THR ASN ALA ILE ILE GLN LEU SEQRES 6 A 658 TYR ARG PHE ILE PRO GLU MET PHE ASN PHE VAL VAL GLY SEQRES 7 A 658 CYS LEU LYS ASP GLU ASN PHE GLU THR THR LEU LEU THR SEQRES 8 A 658 ASP LEU GLY TYR LEU PHE ASP MET MET GLU ARG SER HIS SEQRES 9 A 658 GLY LYS ILE CYS SER SER SER ASN PHE GLN ALA SER LEU SEQRES 10 A 658 LYS SER LEU THR ASP LYS ARG GLN LEU GLU ASN GLY GLU SEQRES 11 A 658 PRO GLN GLU HIS LEU GLU GLU TYR LEU GLU SER LEU CYS SEQRES 12 A 658 ILE ARG GLU SER ILE GLU ASP PHE ASN SER SER GLU SER SEQRES 13 A 658 ILE LYS ARG ASN MET PRO GLN LYS PHE ASN ARG PHE LEU SEQRES 14 A 658 LEU SER GLN LEU ILE LYS GLU GLU ALA GLN THR VAL ASN SEQRES 15 A 658 HIS ASN ILE THR LEU ASN GLN CYS PHE GLY LEU GLU THR SEQRES 16 A 658 GLU ILE ARG THR GLU CYS SER CYS ASP HIS TYR ASP THR SEQRES 17 A 658 THR VAL LYS LEU LEU PRO SER LEU SER ILE SER GLY ILE SEQRES 18 A 658 ASN LYS THR VAL ILE LYS GLN LEU ASN LYS LYS SER ASN SEQRES 19 A 658 GLY GLN ASN ILE LEU PRO TYR ILE GLU TYR ALA MET LYS SEQRES 20 A 658 ASN VAL THR GLN LYS ASN SER ILE CYS PRO THR CYS GLY SEQRES 21 A 658 LYS THR GLU THR ILE THR GLN GLU CYS THR VAL LYS ASN SEQRES 22 A 658 LEU PRO SER VAL LEU SER LEU GLU LEU SER LEU LEU ASP SEQRES 23 A 658 THR GLU PHE SER ASN ILE ARG SER SER LYS ASN TRP LEU SEQRES 24 A 658 THR SER GLU PHE TYR GLY SER ILE ILE LYS ASN LYS ALA SEQRES 25 A 658 VAL LEU ARG SER THR ALA SER GLU LEU LYS GLY THR SER SEQRES 26 A 658 HIS ILE PHE LYS TYR GLU LEU ASN GLY TYR VAL ALA LYS SEQRES 27 A 658 ILE THR ASP ASN ASN ASN GLU THR ARG LEU VAL THR TYR SEQRES 28 A 658 VAL LYS LYS TYR ASN PRO LYS GLU ASN CYS PHE LYS TRP SEQRES 29 A 658 LEU MET PHE ASN ASP TYR LEU VAL VAL GLU ILE THR GLU SEQRES 30 A 658 GLU GLU ALA LEU LYS MET THR TYR PRO TRP LYS THR PRO SEQRES 31 A 658 GLU ILE ILE ILE TYR CYS ASP ALA GLU GLU LEU ARG LYS SEQRES 32 A 658 PRO PHE PHE SER VAL ASP THR TYR SER ILE ASN TYR ASP SEQRES 33 A 658 ILE LEU PHE ARG ASP TYR PHE ALA ASN GLY ILE ARG ASP SEQRES 34 A 658 THR ALA ARG ARG GLU TYR LYS LEU LEU THR HIS ASP GLU SEQRES 35 A 658 ALA PRO LYS SER GLY THR LEU VAL ALA ILE ASP ALA GLU SEQRES 36 A 658 PHE VAL SER LEU GLN SER GLU LEU CYS GLU ILE ASP HIS SEQRES 37 A 658 GLN GLY ILE ARG SER ILE ILE ARG PRO LYS ARG THR ALA SEQRES 38 A 658 LEU ALA ARG ILE SER ILE ILE ARG GLY GLU GLU GLY GLU SEQRES 39 A 658 LEU TYR GLY VAL PRO PHE VAL ASP ASP TYR VAL VAL ASN SEQRES 40 A 658 THR ASN HIS ILE GLU ASP TYR LEU THR ARG TYR SER GLY SEQRES 41 A 658 ILE LEU PRO GLY ASP LEU ASP PRO GLU LYS SER THR LYS SEQRES 42 A 658 ARG LEU VAL ARG ARG ASN VAL VAL TYR ARG LYS VAL TRP SEQRES 43 A 658 LEU LEU MET GLN LEU GLY CYS VAL PHE VAL GLY HIS GLY SEQRES 44 A 658 LEU ASN ASN ASP PHE LYS HIS ILE ASN ILE ASN VAL PRO SEQRES 45 A 658 ARG ASN GLN ILE ARG ASP THR ALA ILE TYR PHE LEU GLN SEQRES 46 A 658 GLY LYS ARG TYR LEU SER LEU ARG TYR LEU ALA TYR VAL SEQRES 47 A 658 LEU LEU GLY MET ASN ILE GLN GLU GLY ASN HIS ASP SER SEQRES 48 A 658 ILE GLU ASP ALA HIS THR ALA LEU ILE LEU TYR LYS LYS SEQRES 49 A 658 TYR LEU HIS LEU LYS GLU LYS ALA ILE PHE GLU LYS VAL SEQRES 50 A 658 LEU ASN SER VAL TYR GLU GLU GLY ARG ALA HIS ASN PHE SEQRES 51 A 658 LYS VAL PRO GLU THR SER LYS GLY HET MG A1201 1 HET MG A1202 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 2(MG 2+) HELIX 1 1 PRO A 476 SER A 480 5 5 HELIX 2 2 TYR A 515 PHE A 525 1 11 HELIX 3 3 ILE A 526 CYS A 536 1 11 HELIX 4 4 LEU A 537 ASP A 539 5 3 HELIX 5 5 THR A 544 HIS A 561 1 18 HELIX 6 6 SER A 567 ASP A 579 1 13 HELIX 7 7 GLU A 594 ILE A 601 1 8 HELIX 8 8 ASN A 617 GLN A 636 1 20 HELIX 9 9 ILE A 642 PHE A 648 1 7 HELIX 10 10 ILE A 695 MET A 703 1 9 HELIX 11 11 LEU A 742 SER A 752 1 11 HELIX 12 12 THR A 833 LYS A 839 1 7 HELIX 13 13 ALA A 855 ARG A 859 1 5 HELIX 14 14 SER A 864 TYR A 868 5 5 HELIX 15 15 TYR A 872 ARG A 877 5 6 HELIX 16 16 THR A 896 ALA A 900 5 5 HELIX 17 17 LEU A 972 GLY A 977 1 6 HELIX 18 18 ASN A 996 GLY A 1009 1 14 HELIX 19 19 GLY A 1016 ASN A 1025 1 10 HELIX 20 20 PRO A 1029 ILE A 1033 5 5 HELIX 21 21 ASP A 1035 PHE A 1040 1 6 HELIX 22 22 SER A 1048 LEU A 1057 1 10 HELIX 23 23 ASP A 1067 LYS A 1088 1 22 HELIX 24 24 ILE A 1090 ASN A 1106 1 17 SHEET 1 A 4 HIS A 662 LEU A 670 0 SHEET 2 A 4 LEU A 650 SER A 659 -1 N THR A 652 O LYS A 668 SHEET 3 A 4 ILE A 722 VAL A 728 -1 O GLU A 725 N ARG A 655 SHEET 4 A 4 LYS A 704 LYS A 709 -1 N THR A 707 O GLN A 724 SHEET 1 B 6 LEU A 673 ILE A 675 0 SHEET 2 B 6 VAL A 734 LEU A 739 1 O SER A 736 N LEU A 673 SHEET 3 B 6 LYS A 845 ASP A 854 -1 O ILE A 850 N LEU A 737 SHEET 4 B 6 PHE A 785 THR A 797 -1 N LYS A 795 O THR A 846 SHEET 5 B 6 GLU A 759 ILE A 765 -1 N PHE A 760 O TYR A 787 SHEET 6 B 6 LYS A 768 ARG A 772 -1 O ARG A 772 N TYR A 761 SHEET 1 C 7 LEU A 673 ILE A 675 0 SHEET 2 C 7 VAL A 734 LEU A 739 1 O SER A 736 N LEU A 673 SHEET 3 C 7 LYS A 845 ASP A 854 -1 O ILE A 850 N LEU A 737 SHEET 4 C 7 PHE A 785 THR A 797 -1 N LYS A 795 O THR A 846 SHEET 5 C 7 THR A 803 ASN A 813 -1 O ARG A 804 N ILE A 796 SHEET 6 C 7 CYS A 818 ASN A 825 -1 O LEU A 822 N VAL A 809 SHEET 7 C 7 LEU A 828 ILE A 832 -1 O LEU A 828 N ASN A 825 SHEET 1 D 5 ARG A 991 LEU A 992 0 SHEET 2 D 5 PRO A 956 VAL A 962 1 N TYR A 961 O LEU A 992 SHEET 3 D 5 THR A 937 ARG A 946 -1 N ALA A 940 O VAL A 962 SHEET 4 D 5 LEU A 906 SER A 915 -1 N VAL A 914 O ALA A 938 SHEET 5 D 5 VAL A1011 VAL A1013 1 O VAL A1013 N VAL A 907 LINK OD1 ASP A 910 MG MG A1201 1555 1555 2.06 LINK OD2 ASP A 910 MG MG A1201 1555 1555 2.21 LINK OD2 ASP A 910 MG MG A1202 1555 1555 2.07 LINK OE2 GLU A 912 MG MG A1201 1555 1555 2.07 LINK OE2 GLU A 912 MG MG A1202 1555 1555 2.00 LINK OD2 ASP A1071 MG MG A1201 1555 1555 2.92 LINK OD2 ASP A1071 MG MG A1202 1555 1555 2.37 CISPEP 1 PHE A 489 GLY A 490 0 -6.28 CISPEP 2 GLY A 490 THR A 491 0 -0.75 CISPEP 3 THR A 491 ASP A 492 0 1.61 CISPEP 4 ARG A 616 ASN A 617 0 0.83 CISPEP 5 SER A 676 GLY A 677 0 7.51 CISPEP 6 ALA A 881 ASN A 882 0 -3.92 CISPEP 7 LYS A 935 ARG A 936 0 2.92 CISPEP 8 LEU A 979 PRO A 980 0 -3.19 CISPEP 9 ARG A 995 ASN A 996 0 -4.53 CISPEP 10 ILE A 1033 ARG A 1034 0 10.75 CISPEP 11 GLU A 1063 GLY A 1064 0 0.22 CISPEP 12 ASN A 1065 HIS A 1066 0 -1.01 SITE 1 AC1 4 ASP A 910 GLU A 912 ASP A1071 MG A1202 SITE 1 AC2 5 ASP A 910 GLU A 912 HIS A1066 ASP A1071 SITE 2 AC2 5 MG A1201 CRYST1 91.712 115.505 257.449 90.00 90.00 90.00 I 2 2 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 0.010904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003884 0.00000