HEADER IMMUNE SYSTEM 16-FEB-17 5UUI TITLE CRYSTAL STRUCTURE OF SPIN-LABELED T77C TNFA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CACHECTIN,TNF-ALPHA,TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY COMPND 5 MEMBER 2,TNF-A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: MTSL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TNF, TNFA, TNFSF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS T77C, TNFA, TNF ALPHA, CYTOKINE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.S.HORANYI,D.M.DRANOW,T.CESKA REVDAT 4 16-OCT-24 5UUI 1 REMARK REVDAT 3 17-JAN-24 5UUI 1 REMARK REVDAT 2 09-AUG-17 5UUI 1 JRNL REVDAT 1 02-AUG-17 5UUI 0 JRNL AUTH B.CARRINGTON,W.K.MYERS,P.HORANYI,M.CALMIANO,A.D.G.LAWSON JRNL TITL NATURAL CONFORMATIONAL SAMPLING OF HUMAN TNF ALPHA JRNL TITL 2 VISUALIZED BY DOUBLE ELECTRON-ELECTRON RESONANCE. JRNL REF BIOPHYS. J. V. 113 371 2017 JRNL REFN ESSN 1542-0086 JRNL PMID 28746848 JRNL DOI 10.1016/J.BPJ.2017.06.007 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2356: ???) 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) : 32.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 26091 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2115 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 10.0030 - 3.4108 0.88 1555 124 0.0937 0.1431 REMARK 3 2 3.4108 - 2.7253 0.89 1574 131 0.1230 0.1561 REMARK 3 3 2.7253 - 2.3862 0.91 1611 116 0.1418 0.1500 REMARK 3 4 2.3862 - 2.1704 0.89 1565 157 0.1528 0.1992 REMARK 3 5 2.1704 - 2.0162 0.90 1601 150 0.1574 0.1808 REMARK 3 6 2.0162 - 1.8982 0.89 1579 159 0.1586 0.1900 REMARK 3 7 1.8982 - 1.8037 0.91 1606 138 0.1621 0.1887 REMARK 3 8 1.8037 - 1.7256 0.93 1650 100 0.1702 0.1492 REMARK 3 9 1.7256 - 1.6595 0.93 1652 126 0.1711 0.2077 REMARK 3 10 1.6595 - 1.6025 0.90 1569 172 0.1830 0.1779 REMARK 3 11 1.6025 - 1.5525 0.91 1602 162 0.1847 0.2006 REMARK 3 12 1.5525 - 1.5083 0.90 1600 166 0.1879 0.1954 REMARK 3 13 1.5083 - 1.4687 0.92 1618 138 0.2135 0.2295 REMARK 3 14 1.4687 - 1.4330 0.92 1643 132 0.2365 0.2338 REMARK 3 15 1.4330 - 1.4005 0.83 1477 145 0.2496 0.2704 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.050 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 : 0.011 1051 REMARK 3 ANGLE : 1.274 1441 REMARK 3 CHIRALITY : 0.093 166 REMARK 3 PLANARITY : 0.005 184 REMARK 3 DIHEDRAL : 18.184 368 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 9 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.7547 57.8178 15.4305 REMARK 3 T TENSOR REMARK 3 T11: 0.0460 T22: 0.1332 REMARK 3 T33: 0.1212 T12: -0.0073 REMARK 3 T13: -0.0218 T23: -0.0380 REMARK 3 L TENSOR REMARK 3 L11: 4.0587 L22: 2.9478 REMARK 3 L33: 4.2639 L12: -0.1275 REMARK 3 L13: -2.1452 L23: -0.6038 REMARK 3 S TENSOR REMARK 3 S11: 0.1653 S12: 0.0823 S13: 0.0414 REMARK 3 S21: -0.0912 S22: -0.0723 S23: -0.2793 REMARK 3 S31: -0.2497 S32: 0.4102 S33: -0.1169 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.0388 61.1427 20.0789 REMARK 3 T TENSOR REMARK 3 T11: 0.0744 T22: 0.1205 REMARK 3 T33: 0.1313 T12: -0.0088 REMARK 3 T13: 0.0010 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 2.6318 L22: 4.3711 REMARK 3 L33: 2.2453 L12: -1.3181 REMARK 3 L13: 1.2440 L23: 1.8567 REMARK 3 S TENSOR REMARK 3 S11: -0.0872 S12: -0.0674 S13: 0.3401 REMARK 3 S21: 0.0944 S22: 0.1223 S23: -0.2935 REMARK 3 S31: -0.0600 S32: 0.1633 S33: -0.0128 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.3269 50.5890 14.6831 REMARK 3 T TENSOR REMARK 3 T11: 0.0581 T22: 0.0701 REMARK 3 T33: 0.0982 T12: 0.0003 REMARK 3 T13: -0.0137 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.2914 L22: 1.1344 REMARK 3 L33: 2.6520 L12: 0.2488 REMARK 3 L13: -0.2855 L23: -0.5578 REMARK 3 S TENSOR REMARK 3 S11: 0.0264 S12: -0.0025 S13: -0.0899 REMARK 3 S21: -0.0146 S22: 0.0325 S23: -0.1148 REMARK 3 S31: 0.1300 S32: 0.0340 S33: -0.0700 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 84 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.7028 44.4627 9.7795 REMARK 3 T TENSOR REMARK 3 T11: 0.1085 T22: 0.0781 REMARK 3 T33: 0.1495 T12: 0.0153 REMARK 3 T13: -0.0052 T23: -0.0239 REMARK 3 L TENSOR REMARK 3 L11: 2.4508 L22: 1.4955 REMARK 3 L33: 2.5401 L12: 0.8623 REMARK 3 L13: -1.0793 L23: 0.5729 REMARK 3 S TENSOR REMARK 3 S11: -0.0671 S12: 0.0690 S13: -0.2601 REMARK 3 S21: 0.0544 S22: 0.0467 S23: -0.2113 REMARK 3 S31: 0.2940 S32: 0.0435 S33: 0.1419 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.0853 54.1139 9.4442 REMARK 3 T TENSOR REMARK 3 T11: 0.0554 T22: 0.0819 REMARK 3 T33: 0.0819 T12: 0.0021 REMARK 3 T13: -0.0028 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.1861 L22: 2.0677 REMARK 3 L33: 5.2718 L12: 0.2446 REMARK 3 L13: -0.9162 L23: -1.9449 REMARK 3 S TENSOR REMARK 3 S11: 0.0600 S12: 0.0870 S13: 0.0433 REMARK 3 S21: -0.0141 S22: 0.0760 S23: -0.0180 REMARK 3 S31: -0.0762 S32: -0.1735 S33: -0.1467 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 127 THROUGH 135 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.4846 44.4644 21.2047 REMARK 3 T TENSOR REMARK 3 T11: 0.1518 T22: 0.1596 REMARK 3 T33: 0.1473 T12: 0.0194 REMARK 3 T13: -0.0597 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 1.1214 L22: 3.2907 REMARK 3 L33: 3.1851 L12: -0.2054 REMARK 3 L13: 0.0015 L23: -2.8919 REMARK 3 S TENSOR REMARK 3 S11: 0.0873 S12: -0.0754 S13: -0.2935 REMARK 3 S21: -0.0464 S22: -0.0583 S23: -0.1627 REMARK 3 S31: 0.4988 S32: 0.5243 S33: 0.3129 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 136 THROUGH 157 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.5529 56.8298 9.2038 REMARK 3 T TENSOR REMARK 3 T11: 0.0397 T22: 0.1004 REMARK 3 T33: 0.1021 T12: -0.0118 REMARK 3 T13: 0.0049 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.3875 L22: 1.2737 REMARK 3 L33: 3.6699 L12: -0.5774 REMARK 3 L13: -0.2677 L23: 1.4859 REMARK 3 S TENSOR REMARK 3 S11: 0.0550 S12: -0.0004 S13: 0.0545 REMARK 3 S21: -0.1028 S22: 0.0245 S23: -0.1077 REMARK 3 S31: -0.1009 S32: 0.1100 S33: -0.0702 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 5UUI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-16 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND [111] REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 32.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.780 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7100 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) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.02 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57200 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1TNF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TNFA (VCID10616, B114005) AT 10 MG/ML REMARK 280 (IN 10 MM HEPES, PH = 7.5, 150 MM NACL) WAS MIXED WITH AN EQUAL REMARK 280 VOLUME OF PROTEIN SOLUTION AND A SOLUTION CONTAINING 24% (W/V) REMARK 280 PEG-4000, 0.24 M MGCL2, 0.05% DDM, AND 0.1 M HEPES/NAOH, PH=8.5. REMARK 280 CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION AT 16 REMARK 280 DEGREES CELSIUS. CRYSTALS WERE THEN SOAKED WITH THE SAME REMARK 280 SOLUTION SUPPLEMENTED WITH 10% MTSL FOR ONE WEEK AND HARVESTED REMARK 280 WITH PARAFFIN OIL., PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 32.83000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.95441 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.03000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 32.83000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 18.95441 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.03000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 32.83000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 18.95441 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.03000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.90882 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.06000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 37.90882 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.06000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 37.90882 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.06000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 98.49000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 56.86323 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 113.72646 REMARK 350 BIOMT3 3 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 351 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 352 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 SER A 0 REMARK 465 VAL A 1 REMARK 465 ARG A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 ARG A 6 REMARK 465 THR A 7 REMARK 465 PRO A 8 REMARK 465 CYS A 69 REMARK 465 PRO A 70 REMARK 465 SER A 71 REMARK 465 THR A 72 REMARK 465 HIS A 73 REMARK 465 CYS A 101 REMARK 465 GLN A 102 REMARK 465 ARG A 103 REMARK 465 GLU A 104 REMARK 465 THR A 105 REMARK 465 PRO A 106 REMARK 465 GLU A 107 REMARK 465 GLY A 108 REMARK 465 ALA A 109 REMARK 465 GLU A 110 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 9 OG REMARK 470 ASP A 10 CG OD1 OD2 REMARK 470 LYS A 11 CG CD CE NZ REMARK 470 GLU A 23 CG CD OE1 OE2 REMARK 470 ARG A 44 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 74 CG1 CG2 REMARK 470 VAL A 85 CG1 CG2 REMARK 470 TYR A 87 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 88 CG CD OE1 NE2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 GLU A 146 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 OD1 ASN A 92 O HOH A 301 2.15 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 CYS A 77 CA - CB - SG ANGL. DEV. = -14.1 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 LEU A 37 89.41 -159.67 REMARK 500 GLN A 88 48.70 -78.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MTN A 200 DBREF 5UUI A 1 157 UNP P01375 TNFA_HUMAN 77 233 SEQADV 5UUI SER A 0 UNP P01375 EXPRESSION TAG SEQADV 5UUI CYS A 77 UNP P01375 THR 153 ENGINEERED MUTATION SEQRES 1 A 158 SER VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 A 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 A 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 A 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 A 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 A 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU CYS SEQRES 7 A 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 A 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 A 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 A 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 A 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 A 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 A 158 ALA LEU HET MTN A 200 12 HETNAM MTN S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3- HETNAM 2 MTN YL)METHYL] METHANESULFONOTHIOATE HETSYN MTN MTSL FORMUL 2 MTN C10 H18 N O3 S2 FORMUL 3 HOH *52(H2 O) HELIX 1 AA1 ARG A 138 LEU A 142 5 5 SHEET 1 AA1 3 TRP A 28 LEU A 29 0 SHEET 2 AA1 3 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 AA1 3 LEU A 36 ALA A 38 -1 O ALA A 38 N VAL A 13 SHEET 1 AA2 5 TRP A 28 LEU A 29 0 SHEET 2 AA2 5 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 AA2 5 TYR A 151 ALA A 156 -1 O PHE A 152 N VAL A 16 SHEET 4 AA2 5 GLY A 54 GLN A 67 -1 N LEU A 57 O ILE A 155 SHEET 5 AA2 5 PRO A 113 LEU A 126 -1 O PHE A 124 N TYR A 56 SHEET 1 AA3 5 GLU A 42 ARG A 44 0 SHEET 2 AA3 5 GLN A 47 VAL A 49 -1 O VAL A 49 N GLU A 42 SHEET 3 AA3 5 ARG A 131 ILE A 136 -1 O LEU A 132 N LEU A 48 SHEET 4 AA3 5 LEU A 76 ILE A 83 -1 N ILE A 83 O ARG A 131 SHEET 5 AA3 5 LYS A 90 LYS A 98 -1 O VAL A 91 N ARG A 82 LINK SG CYS A 77 S1 MTN A 200 1555 1555 2.09 SITE 1 AC1 5 LEU A 75 CYS A 77 SER A 86 ILE A 97 SITE 2 AC1 5 ASN A 137 CRYST1 65.660 65.660 84.090 90.00 90.00 120.00 H 3 9 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 0.015230 0.008793 0.000000 0.00000 SCALE2 0.000000 0.017586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011892 0.00000