HEADER CYTOKINE 05-MAR-08 2ZJC TITLE TNFR1 SELECTVE TNF MUTANT; R1-6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: R1-6, UNP RESIDUES 77-233; COMPND 5 SYNONYM: TNF-ALPHA, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER COMPND 6 2, TNF-A, CACHECTIN; 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 GENE: TNF, TNFA, TNFSF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PYAS(MODIFED FROM PUC VECTOR) KEYWDS PHAGE DISPLAY SYSTEM, TNFR1 SELECTIVITY, TNF, AGONIST, MUTANT, KEYWDS 2 CYTOKINE, LIPOPROTEIN, MEMBRANE, MYRISTATE, PHOSPHOPROTEIN, KEYWDS 3 SECRETED, SIGNAL-ANCHOR, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MUKAI,Y.YAMAGATA,Y.TSUTSUMI REVDAT 4 10-NOV-21 2ZJC 1 REMARK SEQADV REVDAT 3 13-JUL-11 2ZJC 1 VERSN REVDAT 2 03-FEB-09 2ZJC 1 JRNL REVDAT 1 20-JAN-09 2ZJC 0 JRNL AUTH Y.MUKAI,H.SHIBATA,T.NAKAMURA,Y.YOSHIOKA,Y.ABE,T.NOMURA, JRNL AUTH 2 M.TANIAI,T.OHTA,S.IKEMIZU,S.NAKAGAWA,S.TSUNODA,H.KAMADA, JRNL AUTH 3 Y.YAMAGATA,Y.TSUTSUMI JRNL TITL STRUCTURE-FUNCTION RELATIONSHIP OF TUMOR NECROSIS FACTOR JRNL TITL 2 (TNF) AND ITS RECEPTOR INTERACTION BASED ON 3D STRUCTURAL JRNL TITL 3 ANALYSIS OF A FULLY ACTIVE TNFR1-SELECTIVE TNF MUTANT JRNL REF J.MOL.BIOL. V. 385 1221 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19084540 JRNL DOI 10.1016/J.JMB.2008.11.053 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 12060 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 + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1373 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 798 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.4060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3338 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 19.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.17000 REMARK 3 B22 (A**2) : 1.17000 REMARK 3 B33 (A**2) : -1.76000 REMARK 3 B12 (A**2) : 0.59000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.378 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.329 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.501 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3429 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4696 ; 1.271 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 430 ; 6.788 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;38.485 ;24.805 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;19.605 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.308 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 530 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2666 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1488 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2260 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 141 ; 0.157 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 63 ; 0.199 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.191 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2219 ; 0.425 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3506 ; 0.766 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1374 ; 0.938 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1190 ; 1.483 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 157 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5060 19.7770 -2.4510 REMARK 3 T TENSOR REMARK 3 T11: -0.0303 T22: -0.1278 REMARK 3 T33: 0.6965 T12: -0.0072 REMARK 3 T13: 0.0522 T23: -0.0744 REMARK 3 L TENSOR REMARK 3 L11: 7.2741 L22: 5.0031 REMARK 3 L33: 2.1215 L12: -0.7318 REMARK 3 L13: 0.4993 L23: -0.2757 REMARK 3 S TENSOR REMARK 3 S11: 0.1049 S12: 0.4883 S13: -0.7046 REMARK 3 S21: -0.4488 S22: 0.0210 S23: -0.1429 REMARK 3 S31: 0.0590 S32: 0.0964 S33: -0.1259 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 157 REMARK 3 ORIGIN FOR THE GROUP (A): -8.0410 22.0520 17.3240 REMARK 3 T TENSOR REMARK 3 T11: -0.0391 T22: 0.0557 REMARK 3 T33: 0.6702 T12: 0.0665 REMARK 3 T13: 0.0867 T23: 0.1508 REMARK 3 L TENSOR REMARK 3 L11: 8.4563 L22: 2.5695 REMARK 3 L33: 2.5998 L12: 0.3446 REMARK 3 L13: 2.6144 L23: 0.3406 REMARK 3 S TENSOR REMARK 3 S11: -0.0378 S12: -0.6922 S13: -0.7246 REMARK 3 S21: 0.2925 S22: 0.0528 S23: -0.1898 REMARK 3 S31: 0.1934 S32: -0.0944 S33: -0.0150 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 8 C 157 REMARK 3 ORIGIN FOR THE GROUP (A): -3.9240 39.8210 5.1670 REMARK 3 T TENSOR REMARK 3 T11: -0.0377 T22: -0.0837 REMARK 3 T33: 0.6419 T12: 0.0347 REMARK 3 T13: -0.0158 T23: -0.0348 REMARK 3 L TENSOR REMARK 3 L11: 4.6971 L22: 2.8298 REMARK 3 L33: 2.2781 L12: 0.0598 REMARK 3 L13: 0.0282 L23: -0.4122 REMARK 3 S TENSOR REMARK 3 S11: -0.0870 S12: -0.1554 S13: 0.3628 REMARK 3 S21: 0.0194 S22: 0.0632 S23: -0.1324 REMARK 3 S31: -0.1994 S32: -0.0371 S33: 0.0238 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ZJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000028044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-03 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 : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13445 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 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 (%): 38.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K, PH6.5 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 67.93650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.22316 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.34100 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 67.93650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 39.22316 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.34100 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 67.93650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 39.22316 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.34100 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 78.44631 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 38.68200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 78.44631 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 38.68200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 78.44631 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 38.68200 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: 7180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 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: 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 A 9 68.73 -66.59 REMARK 500 THR A 89 105.84 -161.77 REMARK 500 GLN B 21 -38.37 -140.15 REMARK 500 GLU B 23 -40.34 -23.42 REMARK 500 GLU B 110 122.27 -39.01 REMARK 500 PHE B 144 -147.70 55.61 REMARK 500 THR B 147 140.06 -39.72 REMARK 500 SER C 9 -151.14 -135.11 REMARK 500 LEU C 37 87.39 -179.33 REMARK 500 ASP C 45 46.69 35.74 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 GOL B 158 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E7A RELATED DB: PDB REMARK 900 TNF RECEPTOR SUBTYPE ONE-SELECTIVE TNF MUTANT WITH ANTAGONISTIC REMARK 900 ACTIVITY DBREF 2ZJC A 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 2ZJC B 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 2ZJC C 1 157 UNP P01375 TNFA_HUMAN 77 233 SEQADV 2ZJC MET A 11 UNP P01375 LYS 87 ENGINEERED MUTATION SEQADV 2ZJC LYS A 29 UNP P01375 LEU 105 ENGINEERED MUTATION SEQADV 2ZJC ALA A 31 UNP P01375 ARG 107 ENGINEERED MUTATION SEQADV 2ZJC GLY A 32 UNP P01375 ARG 108 ENGINEERED MUTATION SEQADV 2ZJC SER A 65 UNP P01375 LYS 141 ENGINEERED MUTATION SEQADV 2ZJC PRO A 90 UNP P01375 LYS 166 ENGINEERED MUTATION SEQADV 2ZJC ARG A 98 UNP P01375 LYS 174 ENGINEERED MUTATION SEQADV 2ZJC ASN A 112 UNP P01375 LYS 188 ENGINEERED MUTATION SEQADV 2ZJC PRO A 128 UNP P01375 LYS 204 ENGINEERED MUTATION SEQADV 2ZJC SER A 146 UNP P01375 GLU 222 ENGINEERED MUTATION SEQADV 2ZJC THR A 147 UNP P01375 SER 223 ENGINEERED MUTATION SEQADV 2ZJC MET B 11 UNP P01375 LYS 87 ENGINEERED MUTATION SEQADV 2ZJC LYS B 29 UNP P01375 LEU 105 ENGINEERED MUTATION SEQADV 2ZJC ALA B 31 UNP P01375 ARG 107 ENGINEERED MUTATION SEQADV 2ZJC GLY B 32 UNP P01375 ARG 108 ENGINEERED MUTATION SEQADV 2ZJC SER B 65 UNP P01375 LYS 141 ENGINEERED MUTATION SEQADV 2ZJC PRO B 90 UNP P01375 LYS 166 ENGINEERED MUTATION SEQADV 2ZJC ARG B 98 UNP P01375 LYS 174 ENGINEERED MUTATION SEQADV 2ZJC ASN B 112 UNP P01375 LYS 188 ENGINEERED MUTATION SEQADV 2ZJC PRO B 128 UNP P01375 LYS 204 ENGINEERED MUTATION SEQADV 2ZJC SER B 146 UNP P01375 GLU 222 ENGINEERED MUTATION SEQADV 2ZJC THR B 147 UNP P01375 SER 223 ENGINEERED MUTATION SEQADV 2ZJC MET C 11 UNP P01375 LYS 87 ENGINEERED MUTATION SEQADV 2ZJC LYS C 29 UNP P01375 LEU 105 ENGINEERED MUTATION SEQADV 2ZJC ALA C 31 UNP P01375 ARG 107 ENGINEERED MUTATION SEQADV 2ZJC GLY C 32 UNP P01375 ARG 108 ENGINEERED MUTATION SEQADV 2ZJC SER C 65 UNP P01375 LYS 141 ENGINEERED MUTATION SEQADV 2ZJC PRO C 90 UNP P01375 LYS 166 ENGINEERED MUTATION SEQADV 2ZJC ARG C 98 UNP P01375 LYS 174 ENGINEERED MUTATION SEQADV 2ZJC ASN C 112 UNP P01375 LYS 188 ENGINEERED MUTATION SEQADV 2ZJC PRO C 128 UNP P01375 LYS 204 ENGINEERED MUTATION SEQADV 2ZJC SER C 146 UNP P01375 GLU 222 ENGINEERED MUTATION SEQADV 2ZJC THR C 147 UNP P01375 SER 223 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 LYS ASN ALA GLY 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 ALA VAL SER TYR GLN THR 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 SER THR 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 LYS ASN ALA GLY 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 ALA VAL SER TYR GLN THR 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 SER THR 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 LYS ASN ALA GLY 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 ALA VAL SER TYR GLN THR 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 SER THR GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 C 157 LEU HET GOL B 158 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *59(H2 O) HELIX 1 1 ARG A 138 LEU A 142 5 5 HELIX 2 2 ARG C 138 LEU C 142 5 5 SHEET 1 A 3 TRP A 28 LYS A 29 0 SHEET 2 A 3 VAL A 13 ALA A 18 -1 N VAL A 17 O LYS A 29 SHEET 3 A 3 LEU A 36 ALA A 38 -1 O ALA A 38 N VAL A 13 SHEET 1 B 5 TRP A 28 LYS A 29 0 SHEET 2 B 5 VAL A 13 ALA A 18 -1 N VAL A 17 O LYS A 29 SHEET 3 B 5 TYR A 151 LEU A 157 -1 O PHE A 152 N VAL A 16 SHEET 4 B 5 GLY A 54 GLY A 66 -1 N LEU A 55 O LEU A 157 SHEET 5 B 5 TRP A 114 LEU A 126 -1 O LEU A 120 N SER A 60 SHEET 1 C 5 GLU A 42 ARG A 44 0 SHEET 2 C 5 GLN A 47 VAL A 49 -1 O GLN A 47 N ARG A 44 SHEET 3 C 5 ARG A 131 ILE A 136 -1 O LEU A 132 N LEU A 48 SHEET 4 C 5 LEU A 76 ILE A 83 -1 N ILE A 83 O ARG A 131 SHEET 5 C 5 VAL A 91 ARG A 98 -1 O LEU A 93 N ILE A 80 SHEET 1 D 3 GLN B 27 LYS B 29 0 SHEET 2 D 3 VAL B 13 ASN B 19 -1 N VAL B 17 O LYS B 29 SHEET 3 D 3 LEU B 36 ALA B 38 -1 O LEU B 36 N HIS B 15 SHEET 1 E 5 GLN B 27 LYS B 29 0 SHEET 2 E 5 VAL B 13 ASN B 19 -1 N VAL B 17 O LYS B 29 SHEET 3 E 5 TYR B 151 LEU B 157 -1 O PHE B 152 N VAL B 16 SHEET 4 E 5 GLY B 54 GLN B 67 -1 N LEU B 55 O LEU B 157 SHEET 5 E 5 PRO B 113 LEU B 126 -1 O GLY B 122 N ILE B 58 SHEET 1 F 5 GLU B 42 ARG B 44 0 SHEET 2 F 5 GLN B 47 VAL B 49 -1 O VAL B 49 N GLU B 42 SHEET 3 F 5 ARG B 131 ILE B 136 -1 O LEU B 132 N LEU B 48 SHEET 4 F 5 LEU B 76 ILE B 83 -1 N ILE B 83 O ARG B 131 SHEET 5 F 5 VAL B 91 ARG B 98 -1 O ARG B 98 N LEU B 76 SHEET 1 G 3 TRP C 28 LYS C 29 0 SHEET 2 G 3 VAL C 13 ALA C 18 -1 N VAL C 17 O LYS C 29 SHEET 3 G 3 LEU C 36 ALA C 38 -1 O ALA C 38 N VAL C 13 SHEET 1 H 5 TRP C 28 LYS C 29 0 SHEET 2 H 5 VAL C 13 ALA C 18 -1 N VAL C 17 O LYS C 29 SHEET 3 H 5 TYR C 151 ALA C 156 -1 O PHE C 152 N VAL C 16 SHEET 4 H 5 GLY C 54 GLY C 66 -1 N GLN C 61 O TYR C 151 SHEET 5 H 5 TRP C 114 LEU C 126 -1 O PHE C 124 N TYR C 56 SHEET 1 I 5 GLU C 42 ARG C 44 0 SHEET 2 I 5 GLN C 47 VAL C 49 -1 O GLN C 47 N ARG C 44 SHEET 3 I 5 ARG C 131 ILE C 136 -1 O LEU C 132 N LEU C 48 SHEET 4 I 5 LEU C 76 ILE C 83 -1 N THR C 79 O GLU C 135 SHEET 5 I 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 2.04 SSBOND 2 CYS B 69 CYS B 101 1555 1555 2.03 SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.01 CISPEP 1 PHE B 144 ALA B 145 0 -29.33 SITE 1 AC1 7 PRO A 117 ILE A 118 TYR A 119 ARG B 98 SITE 2 AC1 7 ILE B 118 TYR B 119 ARG C 98 CRYST1 135.873 135.873 58.023 90.00 90.00 120.00 H 3 27 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 0.007360 0.004249 0.000000 0.00000 SCALE2 0.000000 0.008498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017235 0.00000