HEADER CYTOKINE 29-JUL-08 2ZPX TITLE TNF RECEPTOR SUBTYPE ONE-SELECTIVE TNF MUTANT WITH ANTAGONISTIC TITLE 2 ACTIVITY; R1ANTTNF-T8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 77-233; COMPND 5 SYNONYM: TNF-ALPHA, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER COMPND 6 2, TNF-A, CACHECTIN, ANTAGONISTIC TNF MUTANT (R1ANTTNF-T8); COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: HUMAN; SOURCE 6 GENE: TNF, TNFA, TNFSF2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PYAS(MODIFIED FROM PUC18) KEYWDS TUMOR NECROSIS FACTOR, TRIMER, ANTAGONISTIC ACTIVITY, TNFR1 SPECIFIC, KEYWDS 2 PHAGE DISPLAY SYSTEM, CYTOKINE, CELL MEMBRANE, LIPOPROTEIN, KEYWDS 3 MEMBRANE, MYRISTATE, PHOSPHOPROTEIN, POLYMORPHISM, SECRETED, SIGNAL- KEYWDS 4 ANCHOR, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MUKAI,T.NAKAMURA,Y.YAMAGATA,Y.TSUTSUMI REVDAT 4 01-NOV-23 2ZPX 1 REMARK REVDAT 3 10-NOV-21 2ZPX 1 SEQADV REVDAT 2 18-AUG-09 2ZPX 1 JRNL REVDAT 1 24-MAR-09 2ZPX 0 JRNL AUTH Y.MUKAI,T.NAKAMURA,Y.YOSHIOKA,H.SHIBATA,Y.ABE,T.NOMURA, JRNL AUTH 2 M.TANIAI,T.OHTA,S.NAKAGAWA,S.TSUNODA,H.KAMADA,Y.YAMAGATA, JRNL AUTH 3 Y.TSUTSUMI JRNL TITL FAST BINDING KINETICS AND CONSERVED 3D STRUCTURE UNDERLIE JRNL TITL 2 THE ANTAGONISTIC ACTIVITY OF MUTANT TNF: USEFUL INFORMATION JRNL TITL 3 FOR DESIGNING ARTIFICIAL PROTEO-ANTAGONISTS JRNL REF J.BIOCHEM. V. 146 167 2009 JRNL REFN ISSN 0021-924X JRNL PMID 19386778 JRNL DOI 10.1093/JB/MVP065 REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1361839.840 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 9762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.309 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1009 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1084 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 121 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.20000 REMARK 3 B22 (A**2) : 3.84000 REMARK 3 B33 (A**2) : -7.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM SIGMAA (A) : 0.56 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.58 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.77 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.15 REMARK 3 BSOL : 80.28 REMARK 3 REMARK 3 NCS MODEL : CONSTR REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2ZPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000028277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10337 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 55.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.24400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.160 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: PDB ENTRY 1TNF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG1500, 0.2M CALCIUM ACETATE, REMARK 280 0.1M SODIUM CACODYLATE, PH6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.79300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.69100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.66550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.69100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.79300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.66550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.4 KCAL/MOL 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 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 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 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 465 VAL B 1 REMARK 465 ARG B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 ARG B 6 REMARK 465 THR B 7 REMARK 465 ARG B 103 REMARK 465 GLU B 104 REMARK 465 THR B 105 REMARK 465 PRO B 106 REMARK 465 GLU B 107 REMARK 465 GLY B 108 REMARK 465 ALA B 109 REMARK 465 GLU B 110 REMARK 465 VAL C 1 REMARK 465 ARG C 2 REMARK 465 SER C 3 REMARK 465 SER C 4 REMARK 465 SER C 5 REMARK 465 ARG C 6 REMARK 465 THR C 7 REMARK 465 ARG C 103 REMARK 465 GLU C 104 REMARK 465 THR C 105 REMARK 465 PRO C 106 REMARK 465 GLU C 107 REMARK 465 GLY C 108 REMARK 465 ALA C 109 REMARK 465 GLU C 110 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 NE2 GLN A 21 NH2 ARG C 31 2554 1.83 REMARK 500 NH2 ARG B 32 OD1 ASP C 10 4445 2.00 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 ARG B 32 N ARG B 32 CA -0.188 REMARK 500 ASN C 34 CB ASN C 34 CG -0.242 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 B 31 CA - C - N ANGL. DEV. = -14.6 DEGREES REMARK 500 ALA B 33 C - N - CA ANGL. DEV. = -23.6 DEGREES REMARK 500 ALA B 33 N - CA - CB ANGL. DEV. = -10.1 DEGREES REMARK 500 ALA B 33 N - CA - C ANGL. DEV. = 41.6 DEGREES REMARK 500 ALA B 33 CA - C - N ANGL. DEV. = -23.4 DEGREES REMARK 500 ALA B 33 O - C - N ANGL. DEV. = 10.7 DEGREES REMARK 500 ASN B 34 CB - CA - C ANGL. DEV. = 15.1 DEGREES REMARK 500 ASN B 34 N - CA - CB ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG C 32 C - N - CA ANGL. DEV. = -21.0 DEGREES REMARK 500 ARG C 32 N - CA - CB ANGL. DEV. = -11.2 DEGREES REMARK 500 ALA C 33 C - N - CA ANGL. DEV. = -16.9 DEGREES REMARK 500 ASN C 34 C - N - CA ANGL. DEV. = -20.0 DEGREES REMARK 500 ASN C 34 N - CA - CB ANGL. DEV. = 31.3 DEGREES REMARK 500 ASN C 34 N - CA - C ANGL. DEV. = -21.9 DEGREES REMARK 500 ALA C 35 N - CA - C ANGL. DEV. = -32.0 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 ASP A 10 -53.09 -169.32 REMARK 500 HIS A 15 72.02 -152.99 REMARK 500 GLU A 23 90.53 -43.85 REMARK 500 ASN A 30 -36.90 -130.94 REMARK 500 ARG A 31 79.73 -62.23 REMARK 500 ALA A 33 -75.44 -41.78 REMARK 500 ASN A 34 38.52 -92.82 REMARK 500 LEU A 37 81.11 172.05 REMARK 500 PRO A 51 -75.97 -83.97 REMARK 500 GLN A 67 76.16 -107.10 REMARK 500 SER A 71 -76.43 -145.32 REMARK 500 THR A 72 -4.17 175.04 REMARK 500 HIS A 73 59.67 -93.62 REMARK 500 ALA A 86 -78.79 -64.01 REMARK 500 ASN A 92 95.07 -64.18 REMARK 500 CYS A 101 175.56 -58.06 REMARK 500 ASN A 112 79.07 64.46 REMARK 500 PRO A 139 7.79 -68.41 REMARK 500 ALA A 145 -70.46 -63.42 REMARK 500 HIS B 15 73.73 -153.11 REMARK 500 ALA B 22 30.22 -80.60 REMARK 500 GLU B 23 89.90 -45.27 REMARK 500 ARG B 32 -139.10 -52.84 REMARK 500 ASN B 34 4.48 -165.46 REMARK 500 LEU B 37 81.89 172.92 REMARK 500 PRO B 51 -74.79 -83.38 REMARK 500 SER B 60 149.36 -172.53 REMARK 500 GLN B 67 76.41 -106.91 REMARK 500 SER B 71 -77.30 -145.03 REMARK 500 THR B 72 -3.29 175.47 REMARK 500 HIS B 73 59.54 -94.18 REMARK 500 ALA B 86 -94.51 -54.35 REMARK 500 ASN B 88 42.32 -84.79 REMARK 500 PRO B 90 170.15 -56.55 REMARK 500 VAL B 91 105.97 -161.14 REMARK 500 PRO B 139 18.14 -66.12 REMARK 500 LEU B 142 103.53 -47.58 REMARK 500 SER C 9 -144.63 -157.67 REMARK 500 ASP C 10 -106.13 -59.35 REMARK 500 HIS C 15 71.43 -154.16 REMARK 500 GLU C 23 89.85 -44.47 REMARK 500 ASN C 30 71.42 -105.27 REMARK 500 ARG C 31 -139.25 -84.54 REMARK 500 LEU C 37 82.57 172.06 REMARK 500 PRO C 51 -74.84 -83.98 REMARK 500 SER C 60 148.78 -176.16 REMARK 500 GLN C 67 76.36 -106.95 REMARK 500 SER C 71 -77.25 -144.54 REMARK 500 THR C 72 -2.65 175.11 REMARK 500 HIS C 73 59.05 -94.38 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. 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 ARG B 32 ALA B 33 -139.63 REMARK 500 ALA B 33 ASN B 34 138.14 REMARK 500 ALA C 33 ASN C 34 126.59 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 ALA C 33 14.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TNF RELATED DB: PDB REMARK 900 RELATED ID: 1TNR RELATED DB: PDB REMARK 900 RELATED ID: 2EA7 RELATED DB: PDB REMARK 900 RELATED ID: 2ZJC RELATED DB: PDB DBREF 2ZPX A 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 2ZPX B 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 2ZPX C 1 157 UNP P01375 TNFA_HUMAN 77 233 SEQADV 2ZPX MET A 11 UNP P01375 LYS 87 ENGINEERED MUTATION SEQADV 2ZPX SER A 65 UNP P01375 LYS 141 ENGINEERED MUTATION SEQADV 2ZPX THR A 84 UNP P01375 ALA 160 ENGINEERED MUTATION SEQADV 2ZPX PRO A 85 UNP P01375 VAL 161 ENGINEERED MUTATION SEQADV 2ZPX ALA A 86 UNP P01375 SER 162 ENGINEERED MUTATION SEQADV 2ZPX ILE A 87 UNP P01375 TYR 163 ENGINEERED MUTATION SEQADV 2ZPX ASN A 88 UNP P01375 GLN 164 ENGINEERED MUTATION SEQADV 2ZPX ARG A 89 UNP P01375 THR 165 ENGINEERED MUTATION SEQADV 2ZPX PRO A 90 UNP P01375 LYS 166 ENGINEERED MUTATION SEQADV 2ZPX ARG A 98 UNP P01375 LYS 174 ENGINEERED MUTATION SEQADV 2ZPX ASN A 112 UNP P01375 LYS 188 ENGINEERED MUTATION SEQADV 2ZPX PRO A 128 UNP P01375 LYS 204 ENGINEERED MUTATION SEQADV 2ZPX MET B 11 UNP P01375 LYS 87 ENGINEERED MUTATION SEQADV 2ZPX SER B 65 UNP P01375 LYS 141 ENGINEERED MUTATION SEQADV 2ZPX THR B 84 UNP P01375 ALA 160 ENGINEERED MUTATION SEQADV 2ZPX PRO B 85 UNP P01375 VAL 161 ENGINEERED MUTATION SEQADV 2ZPX ALA B 86 UNP P01375 SER 162 ENGINEERED MUTATION SEQADV 2ZPX ILE B 87 UNP P01375 TYR 163 ENGINEERED MUTATION SEQADV 2ZPX ASN B 88 UNP P01375 GLN 164 ENGINEERED MUTATION SEQADV 2ZPX ARG B 89 UNP P01375 THR 165 ENGINEERED MUTATION SEQADV 2ZPX PRO B 90 UNP P01375 LYS 166 ENGINEERED MUTATION SEQADV 2ZPX ARG B 98 UNP P01375 LYS 174 ENGINEERED MUTATION SEQADV 2ZPX ASN B 112 UNP P01375 LYS 188 ENGINEERED MUTATION SEQADV 2ZPX PRO B 128 UNP P01375 LYS 204 ENGINEERED MUTATION SEQADV 2ZPX MET C 11 UNP P01375 LYS 87 ENGINEERED MUTATION SEQADV 2ZPX SER C 65 UNP P01375 LYS 141 ENGINEERED MUTATION SEQADV 2ZPX THR C 84 UNP P01375 ALA 160 ENGINEERED MUTATION SEQADV 2ZPX PRO C 85 UNP P01375 VAL 161 ENGINEERED MUTATION SEQADV 2ZPX ALA C 86 UNP P01375 SER 162 ENGINEERED MUTATION SEQADV 2ZPX ILE C 87 UNP P01375 TYR 163 ENGINEERED MUTATION SEQADV 2ZPX ASN C 88 UNP P01375 GLN 164 ENGINEERED MUTATION SEQADV 2ZPX ARG C 89 UNP P01375 THR 165 ENGINEERED MUTATION SEQADV 2ZPX PRO C 90 UNP P01375 LYS 166 ENGINEERED MUTATION SEQADV 2ZPX ARG C 98 UNP P01375 LYS 174 ENGINEERED MUTATION SEQADV 2ZPX ASN C 112 UNP P01375 LYS 188 ENGINEERED MUTATION SEQADV 2ZPX PRO C 128 UNP P01375 LYS 204 ENGINEERED MUTATION SEQRES 1 A 157 VAL ARG SER SER SER ARG THR PRO SER ASP MET PRO VAL SEQRES 2 A 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU SEQRES 3 A 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN SEQRES 4 A 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER SEQRES 5 A 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SER SEQRES 6 A 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS SEQRES 7 A 157 THR ILE SER ARG ILE THR PRO ALA ILE ASN ARG PRO VAL SEQRES 8 A 157 ASN LEU LEU SER ALA ILE ARG SER PRO CYS GLN ARG GLU SEQRES 9 A 157 THR PRO GLU GLY ALA GLU ALA ASN PRO TRP TYR GLU PRO SEQRES 10 A 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU PRO GLY ASP SEQRES 11 A 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP SEQRES 12 A 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 A 157 LEU SEQRES 1 B 157 VAL ARG SER SER SER ARG THR PRO SER ASP MET PRO VAL SEQRES 2 B 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU SEQRES 3 B 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN SEQRES 4 B 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER SEQRES 5 B 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SER SEQRES 6 B 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS SEQRES 7 B 157 THR ILE SER ARG ILE THR PRO ALA ILE ASN ARG PRO VAL SEQRES 8 B 157 ASN LEU LEU SER ALA ILE ARG SER PRO CYS GLN ARG GLU SEQRES 9 B 157 THR PRO GLU GLY ALA GLU ALA ASN PRO TRP TYR GLU PRO SEQRES 10 B 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU PRO GLY ASP SEQRES 11 B 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP SEQRES 12 B 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 B 157 LEU SEQRES 1 C 157 VAL ARG SER SER SER ARG THR PRO SER ASP MET PRO VAL SEQRES 2 C 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU SEQRES 3 C 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN SEQRES 4 C 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER SEQRES 5 C 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SER SEQRES 6 C 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS SEQRES 7 C 157 THR ILE SER ARG ILE THR PRO ALA ILE ASN ARG PRO VAL SEQRES 8 C 157 ASN LEU LEU SER ALA ILE ARG SER PRO CYS GLN ARG GLU SEQRES 9 C 157 THR PRO GLU GLY ALA GLU ALA ASN PRO TRP TYR GLU PRO SEQRES 10 C 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU PRO GLY ASP SEQRES 11 C 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP SEQRES 12 C 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 C 157 LEU FORMUL 4 HOH *7(H2 O) SHEET 1 A 5 LEU A 36 ALA A 38 0 SHEET 2 A 5 VAL A 13 VAL A 17 -1 N VAL A 13 O ALA A 38 SHEET 3 A 5 TYR A 151 ALA A 156 -1 O ILE A 154 N ALA A 14 SHEET 4 A 5 GLY A 54 GLN A 67 -1 N TYR A 59 O GLY A 153 SHEET 5 A 5 PRO A 113 LEU A 126 -1 O LEU A 126 N GLY A 54 SHEET 1 B 5 GLU A 42 LEU A 43 0 SHEET 2 B 5 LEU A 48 VAL A 49 -1 O VAL A 49 N GLU A 42 SHEET 3 B 5 ARG A 131 ILE A 136 -1 O LEU A 132 N LEU A 48 SHEET 4 B 5 LEU A 76 ILE A 83 -1 N THR A 79 O GLU A 135 SHEET 5 B 5 PRO A 90 ARG A 98 -1 O ARG A 98 N LEU A 76 SHEET 1 C 5 LEU B 36 ALA B 38 0 SHEET 2 C 5 VAL B 13 VAL B 17 -1 N VAL B 13 O ALA B 38 SHEET 3 C 5 TYR B 151 ALA B 156 -1 O ILE B 154 N ALA B 14 SHEET 4 C 5 GLY B 54 GLN B 67 -1 N TYR B 59 O GLY B 153 SHEET 5 C 5 PRO B 113 LEU B 126 -1 O LEU B 126 N GLY B 54 SHEET 1 D 5 GLU B 42 LEU B 43 0 SHEET 2 D 5 LEU B 48 VAL B 49 -1 O VAL B 49 N GLU B 42 SHEET 3 D 5 ARG B 131 ILE B 136 -1 O LEU B 132 N LEU B 48 SHEET 4 D 5 LEU B 76 SER B 81 -1 N THR B 79 O GLU B 135 SHEET 5 D 5 ASN B 92 ARG B 98 -1 O ARG B 98 N LEU B 76 SHEET 1 E 5 LEU C 36 ALA C 38 0 SHEET 2 E 5 VAL C 13 VAL C 17 -1 N VAL C 13 O ALA C 38 SHEET 3 E 5 TYR C 151 ALA C 156 -1 O ILE C 154 N ALA C 14 SHEET 4 E 5 GLY C 54 GLN C 67 -1 N TYR C 59 O GLY C 153 SHEET 5 E 5 PRO C 113 LEU C 126 -1 O LEU C 126 N GLY C 54 SHEET 1 F 5 LEU C 36 ALA C 38 0 SHEET 2 F 5 VAL C 13 VAL C 17 -1 N VAL C 13 O ALA C 38 SHEET 3 F 5 TYR C 151 ALA C 156 -1 O ILE C 154 N ALA C 14 SHEET 4 F 5 GLY C 54 GLN C 67 -1 N TYR C 59 O GLY C 153 SHEET 5 F 5 LEU C 142 ASP C 143 -1 O ASP C 143 N LEU C 63 SHEET 1 G 5 GLU C 42 LEU C 43 0 SHEET 2 G 5 LEU C 48 VAL C 49 -1 O VAL C 49 N GLU C 42 SHEET 3 G 5 ARG C 131 ILE C 136 -1 O LEU C 132 N LEU C 48 SHEET 4 G 5 LEU C 76 ILE C 83 -1 N ILE C 83 O ARG C 131 SHEET 5 G 5 VAL C 91 ARG C 98 -1 O ARG C 98 N LEU C 76 SSBOND 1 CYS A 69 CYS A 101 1555 1555 2.03 SSBOND 2 CYS B 69 CYS B 101 1555 1555 2.04 SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.03 CRYST1 49.586 111.331 75.382 90.00 90.00 90.00 P 21 21 21 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 0.020167 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013266 0.00000