HEADER HYDROLASE 10-JAN-20 6TVL TITLE HEN EGG WHITE LYSOZYME IN COMPLEX WITH A "HALF SANDWICH"-TYPE RU(II) TITLE 2 COORDINATION COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 5 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS LYSOZYME, RU(II) COMPLEX, ANTICANCER COMPOUND, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.CHINIADIS,P.GIASTAS,I.BRATSOS,A.PAPAKYRIAKOU REVDAT 3 24-JAN-24 6TVL 1 REMARK REVDAT 2 03-JUN-20 6TVL 1 JRNL REVDAT 1 29-APR-20 6TVL 0 JRNL AUTH L.CHINIADIS,I.BRATSOS,K.BETHANIS,M.KARPUSAS,P.GIASTAS, JRNL AUTH 2 A.PAPAKYRIAKOU JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF A "HALF SANDWICH"-TYPE JRNL TITL 2 RU(II) COORDINATION COMPOUND BOUND TO HEN EGG-WHITE LYSOZYME JRNL TITL 3 AND PROTEINASE K. JRNL REF J.BIOL.INORG.CHEM. V. 25 635 2020 JRNL REFN ESSN 1432-1327 JRNL PMID 32266561 JRNL DOI 10.1007/S00775-020-01786-Z REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 23013 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1132 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 35.4510 - 2.7897 0.99 2931 150 0.1995 0.2296 REMARK 3 2 2.7897 - 2.2143 0.99 2787 150 0.2165 0.2075 REMARK 3 3 2.2143 - 1.9345 0.99 2740 135 0.2237 0.2397 REMARK 3 4 1.9345 - 1.7576 0.99 2723 151 0.2391 0.2941 REMARK 3 5 1.7576 - 1.6316 0.99 2731 137 0.2535 0.2737 REMARK 3 6 1.6316 - 1.5354 0.99 2692 146 0.2660 0.3067 REMARK 3 7 1.5354 - 1.4585 0.97 2665 128 0.2932 0.3416 REMARK 3 8 1.4585 - 1.3950 0.96 2612 135 0.3080 0.3186 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.01 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 72.8995 16.4151 26.6711 REMARK 3 T TENSOR REMARK 3 T11: 0.3229 T22: 0.2594 REMARK 3 T33: 0.4688 T12: 0.0375 REMARK 3 T13: -0.4790 T23: -0.2393 REMARK 3 L TENSOR REMARK 3 L11: 0.4241 L22: 0.2646 REMARK 3 L33: 0.7878 L12: 0.1944 REMARK 3 L13: 0.4122 L23: 0.2616 REMARK 3 S TENSOR REMARK 3 S11: 0.2011 S12: 0.3629 S13: -0.2783 REMARK 3 S21: -0.0845 S22: -0.1013 S23: 0.2963 REMARK 3 S31: 0.1711 S32: -0.2523 S33: -0.0453 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 15 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.8287 23.8353 37.2265 REMARK 3 T TENSOR REMARK 3 T11: 0.1180 T22: 0.2358 REMARK 3 T33: 0.4600 T12: -0.0130 REMARK 3 T13: -0.0454 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 1.2453 L22: 3.9486 REMARK 3 L33: 1.5280 L12: -0.3026 REMARK 3 L13: 0.6445 L23: 0.0851 REMARK 3 S TENSOR REMARK 3 S11: 0.1610 S12: -0.0272 S13: -0.2396 REMARK 3 S21: -0.1115 S22: -0.0094 S23: 0.4218 REMARK 3 S31: 0.2035 S32: -0.2528 S33: -0.1872 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.6858 24.9016 30.2442 REMARK 3 T TENSOR REMARK 3 T11: 0.2404 T22: 0.1712 REMARK 3 T33: 0.2105 T12: 0.0377 REMARK 3 T13: -0.1037 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 1.3266 L22: 0.6470 REMARK 3 L33: 0.4020 L12: -0.5548 REMARK 3 L13: 0.3025 L23: -0.0342 REMARK 3 S TENSOR REMARK 3 S11: 0.1313 S12: 0.1970 S13: -0.3515 REMARK 3 S21: -0.3345 S22: -0.2162 S23: 0.3174 REMARK 3 S31: -0.1437 S32: -0.0333 S33: -0.0039 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 89.6106 18.3289 34.8407 REMARK 3 T TENSOR REMARK 3 T11: 0.1837 T22: 0.1806 REMARK 3 T33: 0.1869 T12: 0.0258 REMARK 3 T13: -0.0568 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 2.1784 L22: 1.0929 REMARK 3 L33: 2.2905 L12: -0.7344 REMARK 3 L13: 1.1502 L23: 0.3946 REMARK 3 S TENSOR REMARK 3 S11: 0.0382 S12: -0.1042 S13: -0.2041 REMARK 3 S21: -0.2340 S22: 0.0434 S23: 0.3027 REMARK 3 S31: -0.1824 S32: 0.0809 S33: -0.0525 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 51 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 86.5136 17.3770 42.5811 REMARK 3 T TENSOR REMARK 3 T11: 0.1803 T22: 0.2351 REMARK 3 T33: 0.1880 T12: 0.0377 REMARK 3 T13: 0.0000 T23: 0.0701 REMARK 3 L TENSOR REMARK 3 L11: 2.3549 L22: 1.9297 REMARK 3 L33: 1.8266 L12: -0.9935 REMARK 3 L13: -0.1644 L23: -0.2583 REMARK 3 S TENSOR REMARK 3 S11: -0.3069 S12: -0.6458 S13: -0.2790 REMARK 3 S21: 0.2823 S22: 0.1253 S23: 0.2422 REMARK 3 S31: -0.0346 S32: 0.1063 S33: 0.1260 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 82.9358 12.7885 43.5006 REMARK 3 T TENSOR REMARK 3 T11: 0.2247 T22: 0.2497 REMARK 3 T33: 0.3937 T12: 0.0547 REMARK 3 T13: 0.0235 T23: 0.0642 REMARK 3 L TENSOR REMARK 3 L11: 1.9493 L22: 0.6455 REMARK 3 L33: 1.8506 L12: -0.4915 REMARK 3 L13: 0.2699 L23: -0.9433 REMARK 3 S TENSOR REMARK 3 S11: -0.0384 S12: -0.5402 S13: -0.5149 REMARK 3 S21: 0.1781 S22: -0.0040 S23: 0.5249 REMARK 3 S31: 0.0898 S32: -0.0731 S33: -0.0724 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 74.3341 18.1998 41.9146 REMARK 3 T TENSOR REMARK 3 T11: 0.1878 T22: 0.2723 REMARK 3 T33: 0.3515 T12: -0.0112 REMARK 3 T13: -0.0173 T23: 0.0606 REMARK 3 L TENSOR REMARK 3 L11: 1.9251 L22: 3.6449 REMARK 3 L33: 1.1615 L12: -0.3115 REMARK 3 L13: -0.1327 L23: 0.6507 REMARK 3 S TENSOR REMARK 3 S11: 0.0697 S12: -0.3072 S13: -0.6037 REMARK 3 S21: 0.3376 S22: 0.1160 S23: 0.2305 REMARK 3 S31: 0.1147 S32: -0.1147 S33: -0.0588 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 114 ) REMARK 3 ORIGIN FOR THE GROUP (A): 79.7529 30.1878 38.4649 REMARK 3 T TENSOR REMARK 3 T11: 0.1811 T22: 0.2201 REMARK 3 T33: 0.1647 T12: -0.0133 REMARK 3 T13: -0.0106 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.0903 L22: 2.0001 REMARK 3 L33: 2.3788 L12: 0.0148 REMARK 3 L13: -0.7262 L23: -0.4172 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: -0.2500 S13: -0.0063 REMARK 3 S21: 0.2426 S22: 0.0493 S23: 0.0041 REMARK 3 S31: -0.2662 S32: 0.3579 S33: -0.1101 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 115 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 73.8871 31.9573 27.4550 REMARK 3 T TENSOR REMARK 3 T11: 0.2823 T22: 0.2287 REMARK 3 T33: 0.1608 T12: 0.0730 REMARK 3 T13: -0.0547 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 2.2794 L22: 1.7114 REMARK 3 L33: 2.8065 L12: 0.5098 REMARK 3 L13: 2.2004 L23: -0.3204 REMARK 3 S TENSOR REMARK 3 S11: 0.2943 S12: 0.3340 S13: -0.2394 REMARK 3 S21: -0.4873 S22: -0.1460 S23: 0.3576 REMARK 3 S31: -0.1684 S32: -0.2257 S33: -0.0332 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 66.6969 22.5798 21.1808 REMARK 3 T TENSOR REMARK 3 T11: 0.5629 T22: 0.4477 REMARK 3 T33: 0.4914 T12: 0.1021 REMARK 3 T13: -0.3129 T23: -0.0939 REMARK 3 L TENSOR REMARK 3 L11: 7.4347 L22: 5.4423 REMARK 3 L33: 6.6427 L12: 5.3904 REMARK 3 L13: 4.0323 L23: 4.9368 REMARK 3 S TENSOR REMARK 3 S11: -0.0491 S12: 0.0388 S13: 0.0021 REMARK 3 S21: -0.1373 S22: 0.2556 S23: 0.6791 REMARK 3 S31: 0.3179 S32: -0.2792 S33: -0.1974 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 6TVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23013 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.395 REMARK 200 RESOLUTION RANGE LOW (A) : 35.451 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02074 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.18110 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.750 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: 193L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL 0.7-1.5 M, 0.1 M NA ACETATE, PH REMARK 280 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 17.95500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.63500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.93250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.63500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.63500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.97750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.63500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.93250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.63500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 8.97750 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 17.95500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 HOH A 355 LIES ON A SPECIAL POSITION. 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 A 302 O HOH A 314 1.86 REMARK 500 O PHE A 3 O HOH A 301 2.04 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 400 O HOH A 407 3645 2.11 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 SER A 81 C ALA A 82 N 0.198 REMARK 500 LEU A 84 C LEU A 84 O 0.149 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 ASP A 101 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES 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 TRP A 62 TRP A 63 -148.91 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 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 86.2 REMARK 620 3 SER A 72 OG 89.0 168.9 REMARK 620 4 ARG A 73 O 92.3 94.0 96.2 REMARK 620 5 HOH A 366 O 99.6 89.7 81.2 167.8 REMARK 620 6 HOH A 378 O 170.3 103.0 81.4 90.2 77.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NYN A 203 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD2 REMARK 620 2 NYN A 203 N2 92.2 REMARK 620 3 NYN A 203 S1 82.3 96.6 REMARK 620 4 NYN A 203 S3 162.7 103.4 88.3 REMARK 620 5 NYN A 203 N1 93.9 85.7 175.5 94.8 REMARK 620 6 NYN A 203 S2 82.3 171.4 89.2 83.1 88.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NYN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TFS A 204 DBREF 6TVL A 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU HET CL A 201 1 HET NA A 202 1 HET NYN A 203 14 HET TFS A 204 8 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM NYN CHLORIDO(1,2-DIAMINOETHANE-K2N,N')(1,4,7- HETNAM 2 NYN TRITHIACYCLONONANE-K3S,S',S'')RUTHENIUM(II) HETNAM 3 NYN TRIFLUOROMETHANESULFONATE HETNAM TFS TRIFLUOROMETHANESULFONIC ACID FORMUL 2 CL CL 1- FORMUL 3 NA NA 1+ FORMUL 4 NYN C8 H16 N2 RU S3 5- FORMUL 5 TFS C H F3 O3 S FORMUL 6 HOH *116(H2 O) HELIX 1 AA1 GLY A 4 HIS A 15 1 12 HELIX 2 AA2 ASN A 19 TYR A 23 5 5 HELIX 3 AA3 SER A 24 ASN A 37 1 14 HELIX 4 AA4 PRO A 79 SER A 85 5 7 HELIX 5 AA5 ILE A 88 SER A 100 1 13 HELIX 6 AA6 ASN A 103 ALA A 107 5 5 HELIX 7 AA7 TRP A 108 CYS A 115 1 8 HELIX 8 AA8 ASP A 119 ILE A 124 5 6 SHEET 1 AA1 3 THR A 43 ARG A 45 0 SHEET 2 AA1 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44 SHEET 3 AA1 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.04 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.20 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.05 LINK O SER A 60 NA NA A 202 1555 1555 2.31 LINK O CYS A 64 NA NA A 202 1555 1555 2.45 LINK OG SER A 72 NA NA A 202 1555 1555 2.36 LINK O ARG A 73 NA NA A 202 1555 1555 2.42 LINK OD2 ASP A 101 RU NYN A 203 1555 1555 1.84 LINK NA NA A 202 O HOH A 366 1555 1555 2.44 LINK NA NA A 202 O HOH A 378 1555 1555 2.33 SITE 1 AC1 2 TYR A 23 ASN A 113 SITE 1 AC2 6 SER A 60 CYS A 64 SER A 72 ARG A 73 SITE 2 AC2 6 HOH A 366 HOH A 378 SITE 1 AC3 7 TRP A 62 TRP A 63 ASP A 101 ASN A 103 SITE 2 AC3 7 ASP A 119 TFS A 204 HOH A 358 SITE 1 AC4 4 ASP A 101 ALA A 122 NYN A 203 HOH A 403 CRYST1 79.270 79.270 35.910 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 0.012615 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027847 0.00000