PDB Short entry for 1DG6 HEADER APOPTOSIS 23-NOV-99 1DG6 TITLE CRYSTAL STRUCTURE OF APO2L/TRAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRIMERIC JELLY-ROLL DOMAIN OF APO2L; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: HUMAN PLACENTA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: TRP PROMOTER; SOURCE 9 OTHER_DETAILS: HUMAN PLACENTA KEYWDS CYTOKINE, TNF, TRIMER, ZINC-BINDING SITE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR S.G.HYMOWITZ,M.P.O'CONNELL,M.H.ULTSCH,A.M.DE VOS,R.F.KELLEY REVDAT 8 09-AUG-23 1DG6 1 REMARK SEQADV LINK REVDAT 7 14-MAR-18 1DG6 1 SEQADV REVDAT 6 13-JUL-11 1DG6 1 VERSN REVDAT 5 24-FEB-09 1DG6 1 VERSN REVDAT 4 01-APR-03 1DG6 1 JRNL REVDAT 3 26-SEP-01 1DG6 1 CRYST1 REVDAT 2 04-FEB-00 1DG6 1 REMARK REVDAT 1 26-JAN-00 1DG6 0 JRNL AUTH S.G.HYMOWITZ,M.P.O'CONNELL,M.H.ULTSCH,A.HURST,K.TOTPAL, JRNL AUTH 2 A.ASHKENAZI,A.M.DE VOS,R.F.KELLEY JRNL TITL A UNIQUE ZINC-BINDING SITE REVEALED BY A HIGH-RESOLUTION JRNL TITL 2 X-RAY STRUCTURE OF HOMOTRIMERIC APO2L/TRAIL. JRNL REF BIOCHEMISTRY V. 39 633 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10651627 JRNL DOI 10.1021/BI992242L REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.141 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3346 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 41840 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.132 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 29975 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 226 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1452.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 13240 REMARK 3 NUMBER OF RESTRAINTS : 16022 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 2.530 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRESTSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED CONJUGANT GRADIENT LEAST SQUARES REMARK 3 AND ANISOTROPIC B-FACTOR REFINEMENT REMARK 4 REMARK 4 1DG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000010058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03321 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 6.40000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 34.0000 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: AMORE REMARK 200 STARTING MODEL: TRUNCATED MODEL OF TNFA PDB CODE 1TNF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION 32% MPD; DROP 1.2MG/ML REMARK 280 APO2L, 20MM TRIS HCL PH 7.5, 1% MPD, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 33.21750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 19.17813 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 65.90900 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 33.21750 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 19.17813 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 65.90900 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 33.21750 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 19.17813 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 65.90900 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 33.21750 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 19.17813 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 65.90900 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 33.21750 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 19.17813 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 65.90900 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 33.21750 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 19.17813 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 65.90900 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 38.35627 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 131.81800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 38.35627 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 131.81800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 38.35627 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 131.81800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 38.35627 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 131.81800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 38.35627 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 131.81800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 38.35627 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 131.81800 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.0 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 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 0.00000 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 ZN ZN A 300 LIES ON A SPECIAL POSITION. REMARK 375 CL CL A 406 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 410 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 433 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 465 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 559 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 565 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 593 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 603 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 611 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 MET A 91 REMARK 465 ILE A 92 REMARK 465 LEU A 93 REMARK 465 ARG A 94 REMARK 465 THR A 95 REMARK 465 SER A 96 REMARK 465 GLU A 97 REMARK 465 GLU A 98 REMARK 465 THR A 99 REMARK 465 ILE A 100 REMARK 465 SER A 101 REMARK 465 THR A 102 REMARK 465 VAL A 103 REMARK 465 GLN A 104 REMARK 465 GLU A 105 REMARK 465 LYS A 106 REMARK 465 GLN A 107 REMARK 465 GLN A 108 REMARK 465 ASN A 109 REMARK 465 ILE A 110 REMARK 465 SER A 111 REMARK 465 PRO A 112 REMARK 465 LEU A 113 REMARK 465 VAL A 114 REMARK 465 ARG A 115 REMARK 465 GLU A 116 REMARK 465 ARG A 117 REMARK 465 GLY A 118 REMARK 465 PRO A 119 REMARK 465 GLY A 131 REMARK 465 ARG A 132 REMARK 465 SER A 133 REMARK 465 ASN A 134 REMARK 465 THR A 135 REMARK 465 LEU A 136 REMARK 465 SER A 137 REMARK 465 SER A 138 REMARK 465 PRO A 139 REMARK 465 ASN A 140 REMARK 465 SER A 141 REMARK 465 GLU A 195 REMARK 465 ILE A 196 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 160 CA GLY A 160 C -0.099 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 ARG A 121 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 149 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 GLY A 160 O - C - N ANGL. DEV. = -17.0 DEGREES REMARK 500 HIS A 161 C - N - CA ANGL. DEV. = -31.9 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 THR A 200 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 227 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 255 CG - CD - NE ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG A 255 CD - NE - CZ ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 255 NE - CZ - NH2 ANGL. DEV. = 5.0 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 ARG A 121 71.03 51.69 REMARK 500 ASN A 202 26.60 42.69 REMARK 500 THR A 214 -153.66 -132.45 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 GLY A 160 HIS A 161 146.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR A 200 22.27 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 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 230 SG REMARK 620 2 CYS A 230 SG 111.7 REMARK 620 3 CYS A 230 SG 111.7 111.7 REMARK 620 4 CL A 406 CL 107.1 107.1 107.1 REMARK 620 5 CL A 406 CL 107.1 107.1 107.1 0.0 REMARK 620 6 CL A 406 CL 107.1 107.1 107.1 0.0 0.0 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 ZN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 406 DBREF 1DG6 A 91 281 UNP P50591 TNF10_HUMAN 91 281 SEQADV 1DG6 ALA A 218 UNP P50591 ASP 218 ENGINEERED MUTATION SEQRES 1 A 191 MET ILE LEU ARG THR SER GLU GLU THR ILE SER THR VAL SEQRES 2 A 191 GLN GLU LYS GLN GLN ASN ILE SER PRO LEU VAL ARG GLU SEQRES 3 A 191 ARG GLY PRO GLN ARG VAL ALA ALA HIS ILE THR GLY THR SEQRES 4 A 191 ARG GLY ARG SER ASN THR LEU SER SER PRO ASN SER LYS SEQRES 5 A 191 ASN GLU LYS ALA LEU GLY ARG LYS ILE ASN SER TRP GLU SEQRES 6 A 191 SER SER ARG SER GLY HIS SER PHE LEU SER ASN LEU HIS SEQRES 7 A 191 LEU ARG ASN GLY GLU LEU VAL ILE HIS GLU LYS GLY PHE SEQRES 8 A 191 TYR TYR ILE TYR SER GLN THR TYR PHE ARG PHE GLN GLU SEQRES 9 A 191 GLU ILE LYS GLU ASN THR LYS ASN ASP LYS GLN MET VAL SEQRES 10 A 191 GLN TYR ILE TYR LYS TYR THR SER TYR PRO ALA PRO ILE SEQRES 11 A 191 LEU LEU MET LYS SER ALA ARG ASN SER CYS TRP SER LYS SEQRES 12 A 191 ASP ALA GLU TYR GLY LEU TYR SER ILE TYR GLN GLY GLY SEQRES 13 A 191 ILE PHE GLU LEU LYS GLU ASN ASP ARG ILE PHE VAL SER SEQRES 14 A 191 VAL THR ASN GLU HIS LEU ILE ASP MET ASP HIS GLU ALA SEQRES 15 A 191 SER PHE PHE GLY ALA PHE LEU VAL GLY HET ZN A 300 1 HET CL A 406 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 HOH *226(H2 O) HELIX 1 1 ASN A 262 HIS A 264 5 3 SHEET 1 A 3 TYR A 237 LEU A 250 0 SHEET 2 A 3 GLY A 180 GLN A 193 -1 O GLY A 180 N LEU A 250 SHEET 3 A 3 ILE A 266 ASP A 267 -1 N ASP A 267 O TYR A 189 SHEET 1 A1 5 TYR A 237 LEU A 250 0 SHEET 2 A1 5 GLY A 180 GLN A 193 -1 O GLY A 180 N LEU A 250 SHEET 3 A1 5 PHE A 274 LEU A 279 -1 N PHE A 274 O GLN A 187 SHEET 4 A1 5 ALA A 123 THR A 127 -1 N ALA A 124 O ALA A 277 SHEET 5 A1 5 PHE A 163 SER A 165 -1 O PHE A 163 N HIS A 125 SHEET 1 B 4 ILE A 220 ASN A 228 0 SHEET 2 B 4 GLN A 205 TYR A 213 -1 N MET A 206 O ARG A 227 SHEET 3 B 4 ARG A 255 VAL A 260 -1 O ARG A 255 N TYR A 213 SHEET 4 B 4 ARG A 149 LYS A 150 -1 N ARG A 149 O VAL A 260 SHEET 1 B1 5 ILE A 220 ASN A 228 0 SHEET 2 B1 5 GLN A 205 TYR A 213 -1 N MET A 206 O ARG A 227 SHEET 3 B1 5 ARG A 255 VAL A 260 -1 O ARG A 255 N TYR A 213 SHEET 4 B1 5 GLU A 173 ILE A 176 -1 O LEU A 174 N ILE A 256 SHEET 5 B1 5 LEU A 167 ARG A 170 -1 O HIS A 168 N VAL A 175 LINK SG CYS A 230 ZN ZN A 300 1555 1555 2.34 LINK SG CYS A 230 ZN ZN A 300 3555 1555 2.34 LINK SG CYS A 230 ZN ZN A 300 2555 1555 2.34 LINK ZN ZN A 300 CL CL A 406 1555 1555 2.34 LINK ZN ZN A 300 CL CL A 406 1555 2555 2.34 LINK ZN ZN A 300 CL CL A 406 1555 3555 2.34 SITE 1 AC1 2 CYS A 230 CL A 406 SITE 1 AC2 2 CYS A 230 ZN A 300 CRYST1 66.435 66.435 197.727 90.00 90.00 120.00 H 3 2 18 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 0.015052 0.008690 0.000000 0.00000 SCALE2 0.000000 0.017381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005057 0.00000