HEADER GENE REGULATION 28-OCT-18 6I1D TITLE STRUCTURE OF THE YSH1-MPE1 NUCLEASE COMPLEX FROM S.CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDORIBONUCLEASE YSH1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YEAST 73 KDA HOMOLOG 1,MRNA 3'-END-PROCESSING PROTEIN YSH1; COMPND 5 EC: 3.1.27.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN MPE1; COMPND 9 CHAIN: B; COMPND 10 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: YSH1, BRR5, YLR277C; SOURCE 8 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMID; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 14 S288C); SOURCE 15 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 16 ORGANISM_TAXID: 559292; SOURCE 17 STRAIN: ATCC 204508 / S288C; SOURCE 18 GENE: MPE1, YKL059C, YKL316; SOURCE 19 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 22 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMID KEYWDS PRE-MRNA, MRNA, NUCLEASE, ENDONUCLEASE, CLEAVAGE, POLYADENYLATION, KEYWDS 2 POLYA, CPF, METALLO-BETA-LACTAMASE, 3' ENDS, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR C.H.HILL,V.BOREIKAITE,A.KUMAR,A.CASANAL,P.KUBIK,G.DEGLIESPOSTI, AUTHOR 2 S.MASLEN,A.MARIANI,O.VON LOEFFELHOLZ,M.GIRBIG,M.SKEHEL,L.A.PASSMORE REVDAT 4 24-JAN-24 6I1D 1 REMARK REVDAT 3 03-APR-19 6I1D 1 JRNL REVDAT 2 20-FEB-19 6I1D 1 JRNL REVDAT 1 13-FEB-19 6I1D 0 JRNL AUTH C.H.HILL,V.BOREIKAITE,A.KUMAR,A.CASANAL,P.KUBIK, JRNL AUTH 2 G.DEGLIESPOSTI,S.MASLEN,A.MARIANI,O.VON LOEFFELHOLZ, JRNL AUTH 3 M.GIRBIG,M.SKEHEL,L.A.PASSMORE JRNL TITL ACTIVATION OF THE ENDONUCLEASE THAT DEFINES MRNA 3' ENDS JRNL TITL 2 REQUIRES INCORPORATION INTO AN 8-SUBUNIT CORE CLEAVAGE AND JRNL TITL 3 POLYADENYLATION FACTOR COMPLEX. JRNL REF MOL.CELL V. 73 1217 2019 JRNL REFN ISSN 1097-2765 JRNL PMID 30737185 JRNL DOI 10.1016/J.MOLCEL.2018.12.023 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 29466 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1487 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 62.1581 - 5.0698 0.98 2583 139 0.1444 0.1582 REMARK 3 2 5.0698 - 4.0243 0.99 2565 106 0.1249 0.1825 REMARK 3 3 4.0243 - 3.5157 0.98 2533 131 0.1538 0.2020 REMARK 3 4 3.5157 - 3.1942 0.99 2532 134 0.1772 0.2379 REMARK 3 5 3.1942 - 2.9653 1.00 2567 129 0.1972 0.2608 REMARK 3 6 2.9653 - 2.7905 0.99 2563 143 0.1989 0.2636 REMARK 3 7 2.7905 - 2.6507 0.98 2501 132 0.2274 0.2879 REMARK 3 8 2.6507 - 2.5353 1.00 2534 141 0.2367 0.2940 REMARK 3 9 2.5353 - 2.4377 0.99 2529 145 0.2661 0.3177 REMARK 3 10 2.4377 - 2.3536 0.99 2562 143 0.2850 0.3278 REMARK 3 11 2.3536 - 2.2800 0.99 2510 144 0.3257 0.3660 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.490 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 : 0.003 4455 REMARK 3 ANGLE : 0.545 6025 REMARK 3 CHIRALITY : 0.046 672 REMARK 3 PLANARITY : 0.003 782 REMARK 3 DIHEDRAL : 11.306 2665 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5951 85.8456 3.0794 REMARK 3 T TENSOR REMARK 3 T11: 0.3039 T22: 0.3441 REMARK 3 T33: 0.5100 T12: 0.0406 REMARK 3 T13: -0.0147 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 3.2082 L22: 1.4502 REMARK 3 L33: 1.6547 L12: 0.2428 REMARK 3 L13: -0.5604 L23: -0.0273 REMARK 3 S TENSOR REMARK 3 S11: 0.0379 S12: -0.1138 S13: 0.2202 REMARK 3 S21: -0.0196 S22: -0.0660 S23: 0.0686 REMARK 3 S31: -0.0920 S32: -0.0578 S33: 0.0085 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 112 THROUGH 167 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4425 80.7286 8.5341 REMARK 3 T TENSOR REMARK 3 T11: 0.3797 T22: 0.4623 REMARK 3 T33: 0.5891 T12: 0.0130 REMARK 3 T13: 0.0083 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 4.8524 L22: 1.3884 REMARK 3 L33: 2.4863 L12: 0.0390 REMARK 3 L13: -0.1312 L23: -0.0812 REMARK 3 S TENSOR REMARK 3 S11: 0.0863 S12: -0.1622 S13: 0.1787 REMARK 3 S21: -0.0462 S22: -0.0208 S23: 0.3074 REMARK 3 S31: -0.1509 S32: -0.1856 S33: -0.0343 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 168 THROUGH 432 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.2526 77.8963 22.6136 REMARK 3 T TENSOR REMARK 3 T11: 0.4063 T22: 0.7024 REMARK 3 T33: 0.4510 T12: 0.0042 REMARK 3 T13: -0.0215 T23: 0.0226 REMARK 3 L TENSOR REMARK 3 L11: 2.9030 L22: 1.4656 REMARK 3 L33: 2.4260 L12: 0.1618 REMARK 3 L13: -0.1667 L23: 0.6484 REMARK 3 S TENSOR REMARK 3 S11: 0.0381 S12: -1.0436 S13: -0.1226 REMARK 3 S21: 0.3315 S22: -0.0450 S23: -0.0992 REMARK 3 S31: 0.1286 S32: 0.0525 S33: -0.0337 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 473 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1505 71.1140 -7.3052 REMARK 3 T TENSOR REMARK 3 T11: 0.3452 T22: 0.4145 REMARK 3 T33: 0.5534 T12: 0.0220 REMARK 3 T13: 0.0753 T23: -0.1441 REMARK 3 L TENSOR REMARK 3 L11: 3.6034 L22: 3.5928 REMARK 3 L33: 3.4244 L12: -0.7346 REMARK 3 L13: 0.8918 L23: -1.0263 REMARK 3 S TENSOR REMARK 3 S11: 0.1164 S12: 0.3195 S13: -0.6305 REMARK 3 S21: -0.3170 S22: -0.0520 S23: -0.1374 REMARK 3 S31: 0.2395 S32: 0.1964 S33: -0.0752 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4370 106.7688 -4.1818 REMARK 3 T TENSOR REMARK 3 T11: 0.3152 T22: 0.3084 REMARK 3 T33: 0.7966 T12: 0.0411 REMARK 3 T13: 0.0778 T23: 0.0766 REMARK 3 L TENSOR REMARK 3 L11: 2.5202 L22: 1.7767 REMARK 3 L33: 3.8891 L12: 2.0838 REMARK 3 L13: 1.7776 L23: 1.1172 REMARK 3 S TENSOR REMARK 3 S11: 0.0238 S12: -0.0859 S13: 0.4455 REMARK 3 S21: 0.5432 S22: 0.2552 S23: 0.6441 REMARK 3 S31: -0.0619 S32: -0.4010 S33: -0.2265 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.1318 118.0320 -3.9352 REMARK 3 T TENSOR REMARK 3 T11: 0.4982 T22: 0.4848 REMARK 3 T33: 0.8970 T12: 0.1099 REMARK 3 T13: 0.1172 T23: 0.1286 REMARK 3 L TENSOR REMARK 3 L11: 5.4261 L22: 9.6998 REMARK 3 L33: 6.0995 L12: 3.8916 REMARK 3 L13: -0.3066 L23: -2.4536 REMARK 3 S TENSOR REMARK 3 S11: 0.1709 S12: 0.0512 S13: 0.3795 REMARK 3 S21: 0.6923 S22: -0.2635 S23: 0.9128 REMARK 3 S31: -0.4751 S32: -0.1947 S33: -0.0016 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 24 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5568 107.8760 -1.4171 REMARK 3 T TENSOR REMARK 3 T11: 0.4308 T22: 0.3947 REMARK 3 T33: 1.0896 T12: -0.0086 REMARK 3 T13: 0.0244 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 4.0000 L22: 8.4501 REMARK 3 L33: 7.2779 L12: -0.2996 REMARK 3 L13: 0.7653 L23: -5.9835 REMARK 3 S TENSOR REMARK 3 S11: 0.1177 S12: -0.0462 S13: 0.7072 REMARK 3 S21: 0.9207 S22: -0.1253 S23: -1.2245 REMARK 3 S31: -0.4562 S32: 0.2986 S33: 0.2695 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 46 THROUGH 52 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8261 101.4666 -9.1641 REMARK 3 T TENSOR REMARK 3 T11: 0.4967 T22: 0.3466 REMARK 3 T33: 0.8549 T12: 0.0746 REMARK 3 T13: 0.0836 T23: 0.0664 REMARK 3 L TENSOR REMARK 3 L11: 5.2704 L22: 2.7383 REMARK 3 L33: 9.4268 L12: -1.0971 REMARK 3 L13: 5.0915 L23: -1.8736 REMARK 3 S TENSOR REMARK 3 S11: 0.2012 S12: 0.1839 S13: 0.1499 REMARK 3 S21: -0.4424 S22: -0.4000 S23: -0.2527 REMARK 3 S31: 0.0456 S32: 0.6286 S33: 0.1960 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 53 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6421 106.9000 -12.8805 REMARK 3 T TENSOR REMARK 3 T11: 0.4179 T22: 0.4207 REMARK 3 T33: 0.6199 T12: 0.0951 REMARK 3 T13: 0.1302 T23: 0.0755 REMARK 3 L TENSOR REMARK 3 L11: 3.7187 L22: 7.1180 REMARK 3 L33: 3.4237 L12: -2.9826 REMARK 3 L13: 0.7131 L23: -2.6022 REMARK 3 S TENSOR REMARK 3 S11: 0.3646 S12: 0.8891 S13: 0.2962 REMARK 3 S21: -0.7298 S22: -0.3988 S23: -0.1345 REMARK 3 S31: 0.1531 S32: -0.0040 S33: -0.0352 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 79 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0181 102.1131 -4.6674 REMARK 3 T TENSOR REMARK 3 T11: 0.4511 T22: 0.5807 REMARK 3 T33: 1.1552 T12: 0.0075 REMARK 3 T13: 0.1133 T23: 0.0609 REMARK 3 L TENSOR REMARK 3 L11: 5.9749 L22: 2.9771 REMARK 3 L33: 5.2454 L12: -2.9996 REMARK 3 L13: 0.0301 L23: -2.5997 REMARK 3 S TENSOR REMARK 3 S11: 0.3086 S12: -0.0194 S13: 0.7118 REMARK 3 S21: -0.6533 S22: 0.2363 S23: -1.8230 REMARK 3 S31: -0.1254 S32: 0.5434 S33: 0.2757 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 6I1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9159 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29524 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 62.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.390 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 1.13000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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: 2I7V, 2C7H REMARK 200 REMARK 200 REMARK: PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80 UL RESERVOIR OF 26 % W/V PEG 3000, REMARK 280 0.1 M CHES PH 8.7 THE FINAL DROP OF 400 NL COMPRISED 200 NL REMARK 280 PROTEIN AND 200 NL CRYSTALLIZATION BUFFER, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 62.13500 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 1 REMARK 465 GLU A 2 REMARK 465 ARG A 3 REMARK 465 THR A 4 REMARK 465 SER A 115 REMARK 465 SER A 116 REMARK 465 SER A 117 REMARK 465 SER A 118 REMARK 465 SER A 119 REMARK 465 MET A 120 REMARK 465 GLY A 121 REMARK 465 THR A 122 REMARK 465 LYS A 123 REMARK 465 ASP A 124 REMARK 465 GLU A 125 REMARK 465 GLY A 474 REMARK 465 MET B 1 REMARK 465 LYS B 82 REMARK 465 SER B 83 REMARK 465 PHE B 84 REMARK 465 SER B 85 REMARK 465 VAL B 86 REMARK 465 HIS B 87 REMARK 465 SER B 88 REMARK 465 ARG B 89 REMARK 465 LEU B 90 REMARK 465 LYS B 91 REMARK 465 GLY B 92 REMARK 465 ASN B 93 REMARK 465 VAL B 94 REMARK 465 GLY B 95 REMARK 465 ALA B 96 REMARK 465 ALA B 97 REMARK 465 ALA B 98 REMARK 465 GLY B 108 REMARK 465 ARG B 109 REMARK 465 PRO B 110 REMARK 465 ARG B 111 REMARK 465 VAL B 112 REMARK 465 LEU B 113 REMARK 465 GLN B 114 REMARK 465 LYS B 115 REMARK 465 ARG B 116 REMARK 465 GLN B 117 REMARK 465 HIS B 118 REMARK 465 THR B 119 REMARK 465 ALA B 120 REMARK 465 THR B 121 REMARK 465 THR B 122 REMARK 465 THR B 123 REMARK 465 ALA B 124 REMARK 465 ASN B 125 REMARK 465 VAL B 126 REMARK 465 SER B 127 REMARK 465 GLY B 128 REMARK 465 THR B 129 REMARK 465 THR B 130 REMARK 465 GLU B 131 REMARK 465 GLU B 132 REMARK 465 GLU B 133 REMARK 465 ARG B 134 REMARK 465 ILE B 135 REMARK 465 ALA B 136 REMARK 465 SER B 137 REMARK 465 MET B 138 REMARK 465 PHE B 139 REMARK 465 ALA B 140 REMARK 465 THR B 141 REMARK 465 GLN B 142 REMARK 465 GLU B 143 REMARK 465 ASN B 144 REMARK 465 GLN B 145 REMARK 465 TRP B 146 REMARK 465 GLU B 147 REMARK 465 GLN B 148 REMARK 465 THR B 149 REMARK 465 GLN B 150 REMARK 465 GLU B 151 REMARK 465 GLU B 152 REMARK 465 MET B 153 REMARK 465 SER B 154 REMARK 465 ALA B 155 REMARK 465 ALA B 156 REMARK 465 THR B 157 REMARK 465 PRO B 158 REMARK 465 VAL B 159 REMARK 465 PHE B 160 REMARK 465 PHE B 161 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 GLY A 340 C GLY A 340 O -0.106 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 CYS A 24 112.16 -168.87 REMARK 500 TYR A 29 119.50 -164.04 REMARK 500 ASP A 37 166.90 68.66 REMARK 500 ALA A 38 79.74 -160.19 REMARK 500 PHE A 137 -51.03 -142.11 REMARK 500 HIS A 163 -84.63 58.18 REMARK 500 HIS A 192 -5.37 -155.44 REMARK 500 SER A 210 36.02 -142.42 REMARK 500 VAL A 274 83.66 56.85 REMARK 500 ASP A 307 -79.15 -56.91 REMARK 500 GLN A 309 8.18 59.11 REMARK 500 SER A 344 -155.95 -166.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 757 DISTANCE = 5.89 ANGSTROMS 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 A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 HIS A 70 ND1 93.6 REMARK 620 3 HIS A 163 NE2 102.8 88.0 REMARK 620 4 ASP A 184 OD2 84.4 169.2 102.8 REMARK 620 5 HOH A 646 O 117.1 101.7 137.9 70.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 72 OD2 REMARK 620 2 HIS A 73 NE2 92.8 REMARK 620 3 ASP A 184 OD2 161.1 85.2 REMARK 620 4 HIS A 430 NE2 95.2 107.2 103.3 REMARK 620 5 HOH A 646 O 76.4 122.1 88.8 130.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 DBREF 6I1D A 1 474 UNP Q06224 YSH1_YEAST 1 474 DBREF 6I1D B 1 161 UNP P35728 MPE1_YEAST 1 160 SEQADV 6I1D LYS B 99 UNP P35728 LEU 98 CONFLICT SEQRES 1 A 474 MET GLU ARG THR ASN THR THR THR PHE LYS PHE PHE SER SEQRES 2 A 474 LEU GLY GLY SER ASN GLU VAL GLY ARG SER CYS HIS ILE SEQRES 3 A 474 LEU GLN TYR LYS GLY LYS THR VAL MET LEU ASP ALA GLY SEQRES 4 A 474 ILE HIS PRO ALA TYR GLN GLY LEU ALA SER LEU PRO PHE SEQRES 5 A 474 TYR ASP GLU PHE ASP LEU SER LYS VAL ASP ILE LEU LEU SEQRES 6 A 474 ILE SER HIS PHE HIS LEU ASP HIS ALA ALA SER LEU PRO SEQRES 7 A 474 TYR VAL MET GLN ARG THR ASN PHE GLN GLY ARG VAL PHE SEQRES 8 A 474 MET THR HIS PRO THR LYS ALA ILE TYR ARG TRP LEU LEU SEQRES 9 A 474 ARG ASP PHE VAL ARG VAL THR SER ILE GLY SER SER SER SEQRES 10 A 474 SER SER MET GLY THR LYS ASP GLU GLY LEU PHE SER ASP SEQRES 11 A 474 GLU ASP LEU VAL ASP SER PHE ASP LYS ILE GLU THR VAL SEQRES 12 A 474 ASP TYR HIS SER THR VAL ASP VAL ASN GLY ILE LYS PHE SEQRES 13 A 474 THR ALA PHE HIS ALA GLY HIS VAL LEU GLY ALA ALA MET SEQRES 14 A 474 PHE GLN ILE GLU ILE ALA GLY LEU ARG VAL LEU PHE THR SEQRES 15 A 474 GLY ASP TYR SER ARG GLU VAL ASP ARG HIS LEU ASN SER SEQRES 16 A 474 ALA GLU VAL PRO PRO LEU SER SER ASN VAL LEU ILE VAL SEQRES 17 A 474 GLU SER THR PHE GLY THR ALA THR HIS GLU PRO ARG LEU SEQRES 18 A 474 ASN ARG GLU ARG LYS LEU THR GLN LEU ILE HIS SER THR SEQRES 19 A 474 VAL MET ARG GLY GLY ARG VAL LEU LEU PRO VAL PHE ALA SEQRES 20 A 474 LEU GLY ARG ALA GLN GLU ILE MET LEU ILE LEU ASP GLU SEQRES 21 A 474 TYR TRP SER GLN HIS ALA ASP GLU LEU GLY GLY GLY GLN SEQRES 22 A 474 VAL PRO ILE PHE TYR ALA SER ASN LEU ALA LYS LYS CYS SEQRES 23 A 474 MET SER VAL PHE GLN THR TYR VAL ASN MET MET ASN ASP SEQRES 24 A 474 ASP ILE ARG LYS LYS PHE ARG ASP SER GLN THR ASN PRO SEQRES 25 A 474 PHE ILE PHE LYS ASN ILE SER TYR LEU ARG ASN LEU GLU SEQRES 26 A 474 ASP PHE GLN ASP PHE GLY PRO SER VAL MET LEU ALA SER SEQRES 27 A 474 PRO GLY MET LEU GLN SER GLY LEU SER ARG ASP LEU LEU SEQRES 28 A 474 GLU ARG TRP CYS PRO GLU ASP LYS ASN LEU VAL LEU ILE SEQRES 29 A 474 THR GLY TYR SER ILE GLU GLY THR MET ALA LYS PHE ILE SEQRES 30 A 474 MET LEU GLU PRO ASP THR ILE PRO SER ILE ASN ASN PRO SEQRES 31 A 474 GLU ILE THR ILE PRO ARG ARG CYS GLN VAL GLU GLU ILE SEQRES 32 A 474 SER PHE ALA ALA HIS VAL ASP PHE GLN GLU ASN LEU GLU SEQRES 33 A 474 PHE ILE GLU LYS ILE SER ALA PRO ASN ILE ILE LEU VAL SEQRES 34 A 474 HIS GLY GLU ALA ASN PRO MET GLY ARG LEU LYS SER ALA SEQRES 35 A 474 LEU LEU SER ASN PHE ALA SER LEU LYS GLY THR ASP ASN SEQRES 36 A 474 GLU VAL HIS VAL PHE ASN PRO ARG ASN CYS VAL GLU VAL SEQRES 37 A 474 ASP LEU GLU PHE GLN GLY SEQRES 1 B 160 MET SER SER THR ILE PHE TYR ARG PHE LYS SER GLN ARG SEQRES 2 B 160 ASN THR SER ARG ILE LEU PHE ASP GLY THR GLY LEU THR SEQRES 3 B 160 VAL PHE ASP LEU LYS ARG GLU ILE ILE GLN GLU ASN LYS SEQRES 4 B 160 LEU GLY ASP GLY THR ASP PHE GLN LEU LYS ILE TYR ASN SEQRES 5 B 160 PRO ASP THR GLU GLU GLU TYR ASP ASP ASP ALA PHE VAL SEQRES 6 B 160 ILE PRO ARG SER THR SER VAL ILE VAL LYS ARG SER PRO SEQRES 7 B 160 ALA ILE LYS SER PHE SER VAL HIS SER ARG LEU LYS GLY SEQRES 8 B 160 ASN VAL GLY ALA ALA ALA LYS GLY ASN ALA THR ARG TYR SEQRES 9 B 160 VAL THR GLY ARG PRO ARG VAL LEU GLN LYS ARG GLN HIS SEQRES 10 B 160 THR ALA THR THR THR ALA ASN VAL SER GLY THR THR GLU SEQRES 11 B 160 GLU GLU ARG ILE ALA SER MET PHE ALA THR GLN GLU ASN SEQRES 12 B 160 GLN TRP GLU GLN THR GLN GLU GLU MET SER ALA ALA THR SEQRES 13 B 160 PRO VAL PHE PHE HET ZN A 501 1 HET ZN A 502 1 HET GOL A 503 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *199(H2 O) HELIX 1 AA1 GLN A 45 LEU A 50 5 6 HELIX 2 AA2 PHE A 52 PHE A 56 5 5 HELIX 3 AA3 ASP A 57 VAL A 61 5 5 HELIX 4 AA4 HIS A 70 ALA A 75 1 6 HELIX 5 AA5 SER A 76 THR A 84 1 9 HELIX 6 AA6 HIS A 94 SER A 112 1 19 HELIX 7 AA7 ASP A 132 PHE A 137 1 6 HELIX 8 AA8 PRO A 219 ARG A 237 1 19 HELIX 9 AA9 ARG A 250 HIS A 265 1 16 HELIX 10 AB1 HIS A 265 GLY A 270 1 6 HELIX 11 AB2 LEU A 282 GLN A 291 1 10 HELIX 12 AB3 THR A 292 MET A 297 5 6 HELIX 13 AB4 ASN A 298 SER A 308 1 11 HELIX 14 AB5 SER A 344 CYS A 355 1 12 HELIX 15 AB6 THR A 372 MET A 378 1 7 HELIX 16 AB7 ASP A 410 SER A 422 1 13 HELIX 17 AB8 GLU A 432 PHE A 447 1 16 HELIX 18 AB9 VAL B 27 ASN B 38 1 12 HELIX 19 AC1 ALA B 102 VAL B 106 5 5 SHEET 1 AA1 7 GLU A 141 VAL A 143 0 SHEET 2 AA1 7 ARG A 89 THR A 93 1 N VAL A 90 O GLU A 141 SHEET 3 AA1 7 ILE A 63 LEU A 65 1 N LEU A 64 O ARG A 89 SHEET 4 AA1 7 LYS A 32 LEU A 36 1 N MET A 35 O LEU A 65 SHEET 5 AA1 7 CYS A 24 TYR A 29 -1 N HIS A 25 O LEU A 36 SHEET 6 AA1 7 THR A 7 GLY A 15 -1 N LEU A 14 O CYS A 24 SHEET 7 AA1 7 VAL A 468 PHE A 472 -1 O LEU A 470 N PHE A 9 SHEET 1 AA2 7 VAL A 149 VAL A 151 0 SHEET 2 AA2 7 ILE A 154 HIS A 160 -1 O PHE A 156 N VAL A 149 SHEET 3 AA2 7 ALA A 168 ILE A 174 -1 O GLU A 173 N LYS A 155 SHEET 4 AA2 7 LEU A 177 PHE A 181 -1 O PHE A 181 N PHE A 170 SHEET 5 AA2 7 VAL A 205 GLU A 209 1 O ILE A 207 N LEU A 180 SHEET 6 AA2 7 ASN A 425 VAL A 429 1 O ILE A 427 N LEU A 206 SHEET 7 AA2 7 HIS A 458 PHE A 460 1 O HIS A 458 N ILE A 426 SHEET 1 AA3 6 ILE A 318 LEU A 321 0 SHEET 2 AA3 6 ILE A 276 ALA A 279 1 N ILE A 276 O SER A 319 SHEET 3 AA3 6 VAL A 334 ALA A 337 1 O LEU A 336 N PHE A 277 SHEET 4 AA3 6 VAL A 241 PRO A 244 1 N LEU A 243 O MET A 335 SHEET 5 AA3 6 LEU A 361 ILE A 364 1 O LEU A 361 N LEU A 242 SHEET 6 AA3 6 GLN A 399 GLU A 402 1 O GLN A 399 N VAL A 362 SHEET 1 AA4 2 THR A 383 PRO A 385 0 SHEET 2 AA4 2 THR A 393 PRO A 395 -1 O ILE A 394 N ILE A 384 SHEET 1 AA5 4 SER B 16 PHE B 20 0 SHEET 2 AA5 4 SER B 3 PHE B 9 -1 N TYR B 7 O SER B 16 SHEET 3 AA5 4 SER B 71 PRO B 78 1 O VAL B 74 N ARG B 8 SHEET 4 AA5 4 PHE B 46 TYR B 51 -1 N GLN B 47 O SER B 77 SHEET 1 AA6 2 GLY B 24 THR B 26 0 SHEET 2 AA6 2 VAL B 65 PRO B 67 -1 O ILE B 66 N LEU B 25 LINK NE2 HIS A 68 ZN ZN A 502 1555 1555 2.59 LINK ND1 HIS A 70 ZN ZN A 502 1555 1555 2.40 LINK OD2 ASP A 72 ZN ZN A 501 1555 1555 2.32 LINK NE2 HIS A 73 ZN ZN A 501 1555 1555 2.32 LINK NE2 HIS A 163 ZN ZN A 502 1555 1555 2.26 LINK OD2 ASP A 184 ZN ZN A 501 1555 1555 2.08 LINK OD2 ASP A 184 ZN ZN A 502 1555 1555 2.56 LINK NE2 HIS A 430 ZN ZN A 501 1555 1555 2.11 LINK ZN ZN A 501 O HOH A 646 1555 1555 2.02 LINK ZN ZN A 502 O HOH A 646 1555 1555 2.43 CISPEP 1 SER A 338 PRO A 339 0 -3.36 SITE 1 AC1 6 ASP A 72 HIS A 73 ASP A 184 HIS A 430 SITE 2 AC1 6 ZN A 502 HOH A 646 SITE 1 AC2 6 HIS A 68 HIS A 70 HIS A 163 ASP A 184 SITE 2 AC2 6 ZN A 501 HOH A 646 SITE 1 AC3 7 LEU A 50 TYR A 53 ASP A 54 TYR A 79 SITE 2 AC3 7 PHE B 9 SER B 11 ARG B 76 CRYST1 43.380 124.270 63.450 90.00 103.21 90.00 P 1 21 1 2 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 0.023052 0.000000 0.005411 0.00000 SCALE2 0.000000 0.008047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016189 0.00000