HEADER DE NOVO PROTEIN 18-APR-23 8SJI TITLE APO STRUCTURE OF COMPUTATIONALLY DESIGNED HOMOTRIMER TP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOPOISOMERASE 1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: TP1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS METALLOPROTEIN, COMPUTATIONAL DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.HOFFNAGLE,F.A.TEZCAN REVDAT 2 12-JUL-23 8SJI 1 JRNL REVDAT 1 05-JUL-23 8SJI 0 JRNL AUTH A.M.HOFFNAGLE,F.A.TEZCAN JRNL TITL ATOMICALLY ACCURATE DESIGN OF METALLOPROTEINS WITH JRNL TITL 2 PREDEFINED COORDINATION GEOMETRIES. JRNL REF J.AM.CHEM.SOC. V. 145 14208 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37352018 JRNL DOI 10.1021/JACS.3C04047 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 48231 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.190 REMARK 3 FREE R VALUE TEST SET COUNT : 3819 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 39.7400 - 4.5100 0.90 3317 142 0.1586 0.1893 REMARK 3 2 4.5100 - 3.5800 0.89 3269 142 0.1301 0.1624 REMARK 3 3 3.5800 - 3.1300 0.84 3079 134 0.1452 0.1855 REMARK 3 4 3.1300 - 2.8400 0.92 3344 143 0.1512 0.2103 REMARK 3 5 2.8400 - 2.6400 0.92 3358 147 0.1537 0.2140 REMARK 3 6 2.6400 - 2.4800 0.87 3217 141 0.1605 0.1793 REMARK 3 7 2.4800 - 2.3600 0.89 3224 139 0.1501 0.1930 REMARK 3 8 2.3600 - 2.2500 0.87 3174 142 0.1533 0.1865 REMARK 3 9 2.2500 - 2.1700 0.86 3168 142 0.1701 0.1710 REMARK 3 10 2.1700 - 2.0900 0.93 3385 147 0.1564 0.2089 REMARK 3 11 2.0900 - 2.0300 0.88 3222 141 0.1813 0.2269 REMARK 3 12 2.0300 - 1.9700 0.85 3132 139 0.1862 0.2420 REMARK 3 13 1.9700 - 1.9200 0.81 2986 135 0.2410 0.2557 REMARK 3 14 1.9200 - 1.8700 0.85 3108 133 0.2479 0.3094 REMARK 3 15 1.8700 - 1.8300 0.92 3368 146 0.1944 0.2119 REMARK 3 16 1.8300 - 1.7900 0.92 3371 147 0.2037 0.2158 REMARK 3 17 1.7900 - 1.7500 0.92 3295 143 0.1962 0.2057 REMARK 3 18 1.7500 - 1.7200 0.91 3363 148 0.2021 0.2475 REMARK 3 19 1.7200 - 1.6900 0.89 3289 143 0.2034 0.2395 REMARK 3 20 1.6900 - 1.6600 0.85 3145 132 0.2270 0.2923 REMARK 3 21 1.6600 - 1.6300 0.89 3157 143 0.2391 0.2757 REMARK 3 22 1.6300 - 1.6100 0.89 3298 146 0.2542 0.2974 REMARK 3 23 1.6100 - 1.5900 0.91 3339 147 0.2468 0.2799 REMARK 3 24 1.5900 - 1.5600 0.91 3334 145 0.2524 0.2860 REMARK 3 25 1.5600 - 1.5400 0.89 3325 148 0.2669 0.3204 REMARK 3 26 1.5400 - 1.5200 0.87 3128 134 0.3551 0.3778 REMARK 3 27 1.5200 - 1.5000 0.80 2927 130 0.3912 0.4738 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.682 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.39 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 : 0.016 2592 REMARK 3 ANGLE : 1.289 3533 REMARK 3 CHIRALITY : 0.085 421 REMARK 3 PLANARITY : 0.009 453 REMARK 3 DIHEDRAL : 22.932 951 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3056 -7.3267 6.4491 REMARK 3 T TENSOR REMARK 3 T11: 0.1305 T22: 0.1578 REMARK 3 T33: 0.1853 T12: 0.0280 REMARK 3 T13: -0.0029 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 1.4097 L22: 6.0249 REMARK 3 L33: 7.6421 L12: 0.0164 REMARK 3 L13: 0.5914 L23: -3.4760 REMARK 3 S TENSOR REMARK 3 S11: 0.0541 S12: 0.1180 S13: -0.1512 REMARK 3 S21: -0.2887 S22: 0.0471 S23: -0.0166 REMARK 3 S31: 0.5572 S32: 0.1870 S33: -0.0507 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 56 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9182 0.9138 10.4277 REMARK 3 T TENSOR REMARK 3 T11: 0.1800 T22: 0.1434 REMARK 3 T33: 0.1761 T12: 0.0095 REMARK 3 T13: 0.0123 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 1.9675 L22: 4.1870 REMARK 3 L33: 4.7373 L12: 0.8676 REMARK 3 L13: -0.8997 L23: -4.2497 REMARK 3 S TENSOR REMARK 3 S11: 0.0485 S12: 0.0263 S13: 0.0061 REMARK 3 S21: 0.0389 S22: 0.1513 S23: 0.2775 REMARK 3 S31: -0.1559 S32: -0.3154 S33: -0.2783 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 81 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8729 -8.8052 9.5822 REMARK 3 T TENSOR REMARK 3 T11: 0.1818 T22: 0.2365 REMARK 3 T33: 0.2395 T12: -0.0186 REMARK 3 T13: -0.0092 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.8571 L22: 2.4386 REMARK 3 L33: 8.9957 L12: -0.0332 REMARK 3 L13: 1.4636 L23: -2.2885 REMARK 3 S TENSOR REMARK 3 S11: 0.0921 S12: -0.1117 S13: -0.1167 REMARK 3 S21: -0.0234 S22: 0.0508 S23: 0.1919 REMARK 3 S31: 0.3060 S32: -0.3241 S33: -0.1899 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4676 8.6474 21.2749 REMARK 3 T TENSOR REMARK 3 T11: 0.1462 T22: 0.2047 REMARK 3 T33: 0.2384 T12: -0.0215 REMARK 3 T13: 0.0262 T23: -0.0452 REMARK 3 L TENSOR REMARK 3 L11: 1.7281 L22: 4.0068 REMARK 3 L33: 4.3133 L12: -1.4598 REMARK 3 L13: 1.4457 L23: -2.5541 REMARK 3 S TENSOR REMARK 3 S11: -0.0827 S12: -0.1660 S13: 0.0084 REMARK 3 S21: 0.0931 S22: 0.0323 S23: 0.3239 REMARK 3 S31: -0.0387 S32: -0.2212 S33: 0.0157 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 56 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9549 11.5057 17.3743 REMARK 3 T TENSOR REMARK 3 T11: 0.1523 T22: 0.1492 REMARK 3 T33: 0.1984 T12: -0.0329 REMARK 3 T13: 0.0012 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 7.5316 L22: 4.0612 REMARK 3 L33: 2.4401 L12: -4.9711 REMARK 3 L13: 3.3179 L23: -1.0877 REMARK 3 S TENSOR REMARK 3 S11: -0.1540 S12: -0.0634 S13: 0.3243 REMARK 3 S21: 0.2219 S22: 0.0310 S23: -0.0247 REMARK 3 S31: -0.4574 S32: 0.0111 S33: 0.3280 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 81 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7270 15.0096 26.4505 REMARK 3 T TENSOR REMARK 3 T11: 0.2426 T22: 0.1936 REMARK 3 T33: 0.3027 T12: -0.0229 REMARK 3 T13: -0.0236 T23: -0.0768 REMARK 3 L TENSOR REMARK 3 L11: 7.6957 L22: 4.4977 REMARK 3 L33: 8.2150 L12: -5.5923 REMARK 3 L13: 4.7582 L23: -3.2632 REMARK 3 S TENSOR REMARK 3 S11: -0.0546 S12: -0.4562 S13: -0.0540 REMARK 3 S21: 0.2670 S22: 0.2692 S23: 0.0849 REMARK 3 S31: -0.0185 S32: -0.0789 S33: -0.0246 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.6614 9.0808 15.7266 REMARK 3 T TENSOR REMARK 3 T11: 0.1547 T22: 0.1836 REMARK 3 T33: 0.1992 T12: -0.0422 REMARK 3 T13: -0.0036 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 2.4569 L22: 4.7066 REMARK 3 L33: 3.6523 L12: -1.4368 REMARK 3 L13: 1.4286 L23: -2.5824 REMARK 3 S TENSOR REMARK 3 S11: -0.0992 S12: 0.0240 S13: 0.2615 REMARK 3 S21: 0.2133 S22: -0.0461 S23: -0.3031 REMARK 3 S31: -0.3428 S32: 0.1525 S33: 0.2001 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 56 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.9539 1.7210 10.1048 REMARK 3 T TENSOR REMARK 3 T11: 0.1541 T22: 0.1747 REMARK 3 T33: 0.1724 T12: -0.0162 REMARK 3 T13: 0.0308 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.2233 L22: 8.1848 REMARK 3 L33: 3.9043 L12: -1.1129 REMARK 3 L13: 0.6104 L23: -4.7641 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: 0.1230 S13: 0.0142 REMARK 3 S21: -0.3143 S22: -0.1147 S23: -0.3183 REMARK 3 S31: 0.0987 S32: 0.1964 S33: 0.0511 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 106 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4536 22.0650 1.7860 REMARK 3 T TENSOR REMARK 3 T11: 0.3750 T22: 0.3408 REMARK 3 T33: 0.4750 T12: -0.0683 REMARK 3 T13: -0.0079 T23: 0.0586 REMARK 3 L TENSOR REMARK 3 L11: 4.5818 L22: 3.9952 REMARK 3 L33: 7.2315 L12: 4.2182 REMARK 3 L13: -5.7409 L23: -5.3579 REMARK 3 S TENSOR REMARK 3 S11: 0.2163 S12: -0.8665 S13: -1.2431 REMARK 3 S21: 0.6697 S22: -0.6551 S23: -0.2151 REMARK 3 S31: -0.0746 S32: 0.4857 S33: 0.4072 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 8SJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48231 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 39.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04643 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.60990 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.330 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 400, 200 MM CACL2, 100 MM TRIS REMARK 280 (PH 8.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 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 47.53000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.53000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.71500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC 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 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 CA CA B 201 LIES ON A SPECIAL POSITION. REMARK 375 CL CL C 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 365 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 368 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 ALA A 108 REMARK 465 GLU A 109 REMARK 465 ASN A 110 REMARK 465 LEU A 111 REMARK 465 TYR A 112 REMARK 465 PHE A 113 REMARK 465 GLN A 114 REMARK 465 GLU B 109 REMARK 465 ASN B 110 REMARK 465 LEU B 111 REMARK 465 TYR B 112 REMARK 465 PHE B 113 REMARK 465 GLN B 114 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR B 96 CA CB OG1 CG2 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 HOH B 301 O HOH B 307 1.84 REMARK 500 O HOH B 375 O HOH B 384 2.00 REMARK 500 O HOH B 339 O HOH B 389 2.04 REMARK 500 O HOH B 404 O HOH C 435 2.06 REMARK 500 O HOH B 343 O HOH B 362 2.09 REMARK 500 OE2 GLU C 56 O HOH C 301 2.09 REMARK 500 O HOH B 362 O HOH B 364 2.11 REMARK 500 OD1 ASP A 50 O HOH A 301 2.13 REMARK 500 N GLN C 1 O HOH C 302 2.14 REMARK 500 O HOH C 433 O HOH C 434 2.14 REMARK 500 OD1 ASP C 5 O HOH C 303 2.14 REMARK 500 O HOH A 304 O HOH A 378 2.15 REMARK 500 OG SER A 52 O HOH A 302 2.16 REMARK 500 O HOH A 311 O HOH A 342 2.16 REMARK 500 O HOH B 307 O HOH B 333 2.17 REMARK 500 O HOH B 302 O HOH B 312 2.19 REMARK 500 O HOH B 305 O HOH B 363 2.19 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 O HOH A 358 O HOH C 429 4546 2.02 REMARK 500 O HOH A 387 O HOH B 325 1554 2.07 REMARK 500 O HOH A 306 O HOH C 349 4546 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 7 CG - SD - CE ANGL. DEV. = -11.8 DEGREES REMARK 500 LEU B 94 CB - CG - CD1 ANGL. DEV. = -10.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER B 107 127.09 56.61 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 B 404 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH B 405 DISTANCE = 7.33 ANGSTROMS REMARK 525 HOH C 434 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH C 435 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH C 436 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH C 437 DISTANCE = 7.87 ANGSTROMS REMARK 525 HOH C 438 DISTANCE = 9.87 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 2 OD1 REMARK 620 2 ASP A 5 OD1 85.9 REMARK 620 3 ASP A 5 OD2 69.2 44.2 REMARK 620 4 GLU C 49 OE1 50.7 106.2 63.9 REMARK 620 5 HOH C 395 O 150.7 114.0 109.2 101.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 5 OD1 REMARK 620 2 GLU B 8 OE1 59.3 REMARK 620 3 GLU B 8 OE2 55.2 6.4 REMARK 620 4 HOH B 302 O 54.8 16.6 10.8 REMARK 620 5 HOH B 343 O 83.6 28.6 29.9 29.0 REMARK 620 6 HOH B 377 O 80.1 21.0 26.2 32.4 19.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 8 OE1 REMARK 620 2 GLU B 8 OE1 0.0 REMARK 620 3 HOH B 303 O 84.7 84.7 REMARK 620 4 HOH B 303 O 79.0 79.0 80.9 REMARK 620 5 HOH B 343 O 108.4 108.4 68.7 147.5 REMARK 620 6 HOH B 343 O 78.6 78.6 147.5 68.7 143.2 REMARK 620 7 HOH B 362 O 81.9 81.9 105.0 159.5 48.0 100.1 REMARK 620 8 HOH B 362 O 115.7 115.7 159.4 104.9 100.0 48.0 76.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 18 OE1 REMARK 620 2 LYS C 19 O 65.0 REMARK 620 3 ASP C 21 OD1 80.7 15.7 REMARK 620 4 ASP C 21 OD2 74.5 9.5 6.8 REMARK 620 5 HOH C 340 O 79.5 16.1 8.9 7.9 REMARK 620 6 HOH C 347 O 83.1 22.2 15.0 14.8 7.0 REMARK 620 7 HOH C 373 O 61.0 6.5 20.9 14.1 18.6 23.3 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8SJF RELATED DB: PDB REMARK 900 RELATED ID: 8SJG RELATED DB: PDB REMARK 900 RELATED ID: 8SJH RELATED DB: PDB DBREF 8SJI A 1 114 PDB 8SJI 8SJI 1 114 DBREF 8SJI B 1 114 PDB 8SJI 8SJI 1 114 DBREF 8SJI C 1 114 PDB 8SJI 8SJI 1 114 SEQRES 1 A 114 GLN ASP TRP GLU ASP ALA MET GLU THR LEU ASN ASP ASN SEQRES 2 A 114 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ASP GLN VAL SEQRES 3 A 114 ILE ALA ALA LEU LEU TYR MET LEU ALA ALA ALA ILE ALA SEQRES 4 A 114 ALA ALA THR ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 114 PRO THR SER GLU GLU ALA LEU ALA PHE ARG LEU GLY MET SEQRES 6 A 114 HIS GLU LEU ALA ALA LEU ILE THR LYS ALA THR ALA LEU SEQRES 7 A 114 ALA TYR GLN GLY LEU VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 114 GLU GLN LEU LYS THR THR VAL ASN ALA HIS TRP GLN LYS SEQRES 9 A 114 TYR ARG SER ALA GLU ASN LEU TYR PHE GLN SEQRES 1 B 114 GLN ASP TRP GLU ASP ALA MET GLU THR LEU ASN ASP ASN SEQRES 2 B 114 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ASP GLN VAL SEQRES 3 B 114 ILE ALA ALA LEU LEU TYR MET LEU ALA ALA ALA ILE ALA SEQRES 4 B 114 ALA ALA THR ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 B 114 PRO THR SER GLU GLU ALA LEU ALA PHE ARG LEU GLY MET SEQRES 6 B 114 HIS GLU LEU ALA ALA LEU ILE THR LYS ALA THR ALA LEU SEQRES 7 B 114 ALA TYR GLN GLY LEU VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 B 114 GLU GLN LEU LYS THR THR VAL ASN ALA HIS TRP GLN LYS SEQRES 9 B 114 TYR ARG SER ALA GLU ASN LEU TYR PHE GLN SEQRES 1 C 114 GLN ASP TRP GLU ASP ALA MET GLU THR LEU ASN ASP ASN SEQRES 2 C 114 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ASP GLN VAL SEQRES 3 C 114 ILE ALA ALA LEU LEU TYR MET LEU ALA ALA ALA ILE ALA SEQRES 4 C 114 ALA ALA THR ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 C 114 PRO THR SER GLU GLU ALA LEU ALA PHE ARG LEU GLY MET SEQRES 6 C 114 HIS GLU LEU ALA ALA LEU ILE THR LYS ALA THR ALA LEU SEQRES 7 C 114 ALA TYR GLN GLY LEU VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 C 114 GLU GLN LEU LYS THR THR VAL ASN ALA HIS TRP GLN LYS SEQRES 9 C 114 TYR ARG SER ALA GLU ASN LEU TYR PHE GLN HET CA A 201 1 HET CA B 201 1 HET CA B 202 1 HET CA C 201 1 HET CL C 202 1 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 4 CA 4(CA 2+) FORMUL 8 CL CL 1- FORMUL 9 HOH *339(H2 O) HELIX 1 AA1 ASP A 2 ALA A 20 1 19 HELIX 2 AA2 ASN A 22 ALA A 43 1 22 HELIX 3 AA3 PRO A 45 GLU A 49 5 5 HELIX 4 AA4 SER A 55 GLN A 81 1 27 HELIX 5 AA5 LEU A 83 ARG A 106 1 24 HELIX 6 AA6 ASP B 2 ALA B 20 1 19 HELIX 7 AA7 ASN B 22 THR B 42 1 21 HELIX 8 AA8 PRO B 45 GLU B 49 5 5 HELIX 9 AA9 SER B 55 GLN B 81 1 27 HELIX 10 AB1 LEU B 83 ARG B 106 1 24 HELIX 11 AB2 ASP C 2 ALA C 20 1 19 HELIX 12 AB3 ASN C 22 ALA C 43 1 22 HELIX 13 AB4 PRO C 45 GLU C 49 5 5 HELIX 14 AB5 SER C 55 GLN C 81 1 27 HELIX 15 AB6 LEU C 83 ARG C 106 1 24 HELIX 16 AB7 ALA C 108 TYR C 112 5 5 LINK OD1 ASP A 2 CA CA A 201 1555 1555 2.49 LINK OD1 ASP A 5 CA CA A 201 1555 1555 3.08 LINK OD2 ASP A 5 CA CA A 201 1555 1555 2.41 LINK CA CA A 201 OE1 GLU C 49 4555 1555 2.28 LINK CA CA A 201 O HOH C 395 1555 4545 2.44 LINK OD1 ASP B 5 CA CA B 202 1555 2556 2.35 LINK OE1 GLU B 8 CA CA B 201 1555 1555 2.34 LINK OE1 GLU B 8 CA CA B 201 1555 2556 2.34 LINK OE1 GLU B 8 CA CA B 202 1555 1555 3.09 LINK OE2 GLU B 8 CA CA B 202 1555 1555 2.50 LINK CA CA B 201 O HOH B 303 1555 1555 2.29 LINK CA CA B 201 O HOH B 303 1555 2556 2.29 LINK CA CA B 201 O HOH B 343 1555 1555 2.62 LINK CA CA B 201 O HOH B 343 1555 2556 2.62 LINK CA CA B 201 O HOH B 362 1555 1555 2.52 LINK CA CA B 201 O HOH B 362 1555 2556 2.52 LINK CA CA B 202 O HOH B 302 1555 1555 3.19 LINK CA CA B 202 O HOH B 343 1555 2556 2.49 LINK CA CA B 202 O HOH B 377 1555 1555 2.43 LINK OE1 GLU C 18 CA CA C 201 1555 2656 2.40 LINK O LYS C 19 CA CA C 201 1555 1555 2.35 LINK OD1 ASP C 21 CA CA C 201 1555 1555 2.70 LINK OD2 ASP C 21 CA CA C 201 1555 1555 2.84 LINK CA CA C 201 O HOH C 340 1555 1555 2.34 LINK CA CA C 201 O HOH C 347 1555 2656 2.34 LINK CA CA C 201 O HOH C 373 1555 1555 2.85 CRYST1 95.060 77.430 47.440 90.00 106.58 90.00 C 1 2 1 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 0.010520 0.000000 0.003133 0.00000 SCALE2 0.000000 0.012915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021994 0.00000