PDB Short entry for 3K51 HEADER IMMUNE SYSTEM 06-OCT-09 3K51 TITLE CRYSTAL STRUCTURE OF DCR3-TL1A COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 15, COMPND 3 SECRETED FORM; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH INHIBITOR, TNF LIGAND- COMPND 6 RELATED MOLECULE 1, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER COMPND 7 15, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER COMPND 8 15, SECRETED FORM; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: DECOY RECEPTOR 3; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: TNFR CYSTEINE RICH DOMAIN; COMPND 15 SYNONYM: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 6B, DECOY COMPND 16 RECEPTOR FOR FAS LIGAND, DCR3, M68; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TL1, TNFSF15, VEGI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-AI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: DCR3, TNFRSF6B, TR6, UNQ186/PRO212; SOURCE 16 EXPRESSION_SYSTEM: DROSOPHILA; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7215; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: S2; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PMT/BIP/V5-HIS KEYWDS DCR3, TL1A, TNF, TNFR, DECOY RECEPTOR, IMMUNITY, CYTOKINE, DISULFIDE KEYWDS 2 BOND, GLYCOPROTEIN, MEMBRANE, SECRETED, SIGNAL-ANCHOR, KEYWDS 3 TRANSMEMBRANE, APOPTOSIS, RECEPTOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.ZHAN,Y.PATSKOVSKY,Q.YAN,Z.LI,U.A.RAMAGOPAL,S.G.NATHENSON,S.C.ALMO REVDAT 5 06-SEP-23 3K51 1 REMARK REVDAT 4 13-OCT-21 3K51 1 SEQADV REVDAT 3 01-NOV-17 3K51 1 REMARK REVDAT 2 23-FEB-11 3K51 1 JRNL REVDAT 1 13-OCT-10 3K51 0 JRNL AUTH C.ZHAN,Y.PATSKOVSKY,Q.YAN,Z.LI,U.RAMAGOPAL,H.CHENG, JRNL AUTH 2 M.BRENOWITZ,X.HUI,S.G.NATHENSON,S.C.ALMO JRNL TITL DECOY STRATEGIES: THE STRUCTURE OF TL1A:DCR3 COMPLEX. JRNL REF STRUCTURE V. 19 162 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21300286 JRNL DOI 10.1016/J.STR.2010.12.004 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17779 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 566 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1227 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2339 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 83 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.27000 REMARK 3 B22 (A**2) : -3.27000 REMARK 3 B33 (A**2) : 4.90000 REMARK 3 B12 (A**2) : -1.63000 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): 0.324 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.247 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.163 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.811 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2460 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3363 ; 0.540 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 313 ; 6.262 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;27.375 ;22.909 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 370 ;15.111 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.151 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 362 ; 0.048 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1919 ; 0.004 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 970 ; 0.193 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1669 ; 0.319 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 222 ; 0.201 ; 0.500 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): 62 ; 0.136 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.153 ; 0.500 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): 1543 ; 2.194 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2499 ; 3.909 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 917 ; 4.026 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 857 ; 5.970 ; 6.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: EXTRA ELECTRON DENSITY POSSIBLY REMARK 3 CORRESPONDING TO N-GLYCAN IS OBSERVED CLOSE TO N173 IN CHAIN B. REMARK 3 BECAUSE OF THE DYNAMIC STRUCTURAL FEATURES, THIS DENSITY IS TOO REMARK 3 WEAK FOR ACCURATE MODELING OF GLYCANS. REMARK 4 REMARK 4 3K51 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-08 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17791 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 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 : 7.700 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.99000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.170 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: PDB ENTRY 2QE3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH6.5, 8% PEG 10K, 3% DEXTRAN REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 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 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 LEU A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 465 PHE A 10 REMARK 465 ALA A 11 REMARK 465 PRO A 12 REMARK 465 SER A 13 REMARK 465 HIS A 14 REMARK 465 GLN A 15 REMARK 465 GLN A 16 REMARK 465 VAL A 17 REMARK 465 TYR A 18 REMARK 465 ALA A 19 REMARK 465 PRO A 20 REMARK 465 LEU A 21 REMARK 465 ARG A 22 REMARK 465 ALA A 23 REMARK 465 ASP A 24 REMARK 465 THR A 92 REMARK 465 SER A 93 REMARK 465 GLU A 94 REMARK 465 SER A 95 REMARK 465 SER A 96 REMARK 465 GLU A 97 REMARK 465 ILE A 98 REMARK 465 ARG A 99 REMARK 465 GLN A 100 REMARK 465 ALA A 101 REMARK 465 GLY A 102 REMARK 465 ARG A 103 REMARK 465 PRO A 104 REMARK 465 ASN A 105 REMARK 465 LYS A 106 REMARK 465 GLU A 136 REMARK 465 VAL A 137 REMARK 465 ARG B 28 REMARK 465 SER B 29 REMARK 465 VAL B 30 REMARK 465 ALA B 31 REMARK 465 THR B 43 REMARK 465 GLY B 44 REMARK 465 SER B 195 REMARK 465 THR B 196 REMARK 465 GLY B 197 REMARK 465 HIS B 198 REMARK 465 HIS B 199 REMARK 465 HIS B 200 REMARK 465 HIS B 201 REMARK 465 HIS B 202 REMARK 465 HIS B 203 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 GLN A 41 CG CD OE1 NE2 REMARK 470 HIS A 42 CG ND1 CD2 CE1 NE2 REMARK 470 PHE A 43 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 ASN A 45 CG OD1 ND2 REMARK 470 GLN A 46 CG CD OE1 NE2 REMARK 470 ARG B 64 CD NE CZ NH1 NH2 REMARK 470 ASP B 65 CG OD1 OD2 REMARK 470 LEU B 181 CG CD1 CD2 REMARK 470 VAL B 183 CG1 CG2 REMARK 470 SER B 187 OG 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 PRO B 184 C - N - CD ANGL. DEV. = -24.6 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 ASN A 45 -5.03 82.84 REMARK 500 GLU A 55 -16.64 -147.16 REMARK 500 ARG A 64 -1.22 84.77 REMARK 500 LYS A 70 -15.55 95.11 REMARK 500 CYS B 91 89.39 -67.22 REMARK 500 GLU B 97 -126.31 58.95 REMARK 500 PRO B 144 -7.75 -45.77 REMARK 500 PRO B 155 119.23 -35.40 REMARK 500 SER B 162 41.87 -109.77 REMARK 500 HIS B 189 4.46 83.85 REMARK 500 ASP B 190 -131.78 57.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QE3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TL1A DBREF 3K51 A 5 184 UNP O95150 TNF15_HUMAN 72 251 DBREF 3K51 B 30 195 UNP O95407 TNF6B_HUMAN 30 195 SEQADV 3K51 GLY A 1 UNP O95150 EXPRESSION TAG SEQADV 3K51 SER A 2 UNP O95150 EXPRESSION TAG SEQADV 3K51 HIS A 3 UNP O95150 EXPRESSION TAG SEQADV 3K51 MET A 4 UNP O95150 EXPRESSION TAG SEQADV 3K51 SER A 95 UNP O95150 CYS 162 ENGINEERED MUTATION SEQADV 3K51 SER A 135 UNP O95150 CYS 202 ENGINEERED MUTATION SEQADV 3K51 ARG B 28 UNP O95407 EXPRESSION TAG SEQADV 3K51 SER B 29 UNP O95407 EXPRESSION TAG SEQADV 3K51 THR B 196 UNP O95407 EXPRESSION TAG SEQADV 3K51 GLY B 197 UNP O95407 EXPRESSION TAG SEQADV 3K51 HIS B 198 UNP O95407 EXPRESSION TAG SEQADV 3K51 HIS B 199 UNP O95407 EXPRESSION TAG SEQADV 3K51 HIS B 200 UNP O95407 EXPRESSION TAG SEQADV 3K51 HIS B 201 UNP O95407 EXPRESSION TAG SEQADV 3K51 HIS B 202 UNP O95407 EXPRESSION TAG SEQADV 3K51 HIS B 203 UNP O95407 EXPRESSION TAG SEQRES 1 A 184 GLY SER HIS MET LEU LYS GLY GLN GLU PHE ALA PRO SER SEQRES 2 A 184 HIS GLN GLN VAL TYR ALA PRO LEU ARG ALA ASP GLY ASP SEQRES 3 A 184 LYS PRO ARG ALA HIS LEU THR VAL VAL ARG GLN THR PRO SEQRES 4 A 184 THR GLN HIS PHE LYS ASN GLN PHE PRO ALA LEU HIS TRP SEQRES 5 A 184 GLU HIS GLU LEU GLY LEU ALA PHE THR LYS ASN ARG MET SEQRES 6 A 184 ASN TYR THR ASN LYS PHE LEU LEU ILE PRO GLU SER GLY SEQRES 7 A 184 ASP TYR PHE ILE TYR SER GLN VAL THR PHE ARG GLY MET SEQRES 8 A 184 THR SER GLU SER SER GLU ILE ARG GLN ALA GLY ARG PRO SEQRES 9 A 184 ASN LYS PRO ASP SER ILE THR VAL VAL ILE THR LYS VAL SEQRES 10 A 184 THR ASP SER TYR PRO GLU PRO THR GLN LEU LEU MET GLY SEQRES 11 A 184 THR LYS SER VAL SER GLU VAL GLY SER ASN TRP PHE GLN SEQRES 12 A 184 PRO ILE TYR LEU GLY ALA MET PHE SER LEU GLN GLU GLY SEQRES 13 A 184 ASP LYS LEU MET VAL ASN VAL SER ASP ILE SER LEU VAL SEQRES 14 A 184 ASP TYR THR LYS GLU ASP LYS THR PHE PHE GLY ALA PHE SEQRES 15 A 184 LEU LEU SEQRES 1 B 176 ARG SER VAL ALA GLU THR PRO THR TYR PRO TRP ARG ASP SEQRES 2 B 176 ALA GLU THR GLY GLU ARG LEU VAL CYS ALA GLN CYS PRO SEQRES 3 B 176 PRO GLY THR PHE VAL GLN ARG PRO CYS ARG ARG ASP SER SEQRES 4 B 176 PRO THR THR CYS GLY PRO CYS PRO PRO ARG HIS TYR THR SEQRES 5 B 176 GLN PHE TRP ASN TYR LEU GLU ARG CYS ARG TYR CYS ASN SEQRES 6 B 176 VAL LEU CYS GLY GLU ARG GLU GLU GLU ALA ARG ALA CYS SEQRES 7 B 176 HIS ALA THR HIS ASN ARG ALA CYS ARG CYS ARG THR GLY SEQRES 8 B 176 PHE PHE ALA HIS ALA GLY PHE CYS LEU GLU HIS ALA SER SEQRES 9 B 176 CYS PRO PRO GLY ALA GLY VAL ILE ALA PRO GLY THR PRO SEQRES 10 B 176 SER GLN ASN THR GLN CYS GLN PRO CYS PRO PRO GLY THR SEQRES 11 B 176 PHE SER ALA SER SER SER SER SER GLU GLN CYS GLN PRO SEQRES 12 B 176 HIS ARG ASN CYS THR ALA LEU GLY LEU ALA LEU ASN VAL SEQRES 13 B 176 PRO GLY SER SER SER HIS ASP THR LEU CYS THR SER THR SEQRES 14 B 176 GLY HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *83(H2 O) HELIX 1 1 ASP A 165 VAL A 169 5 5 HELIX 2 2 ASN B 173 GLY B 178 1 6 SHEET 1 A 3 TRP A 52 GLU A 53 0 SHEET 2 A 3 ARG A 29 VAL A 34 -1 N THR A 33 O GLU A 53 SHEET 3 A 3 PHE A 60 LYS A 62 -1 O LYS A 62 N ARG A 29 SHEET 1 B 5 TRP A 52 GLU A 53 0 SHEET 2 B 5 ARG A 29 VAL A 34 -1 N THR A 33 O GLU A 53 SHEET 3 B 5 PHE A 178 LEU A 183 -1 O PHE A 179 N LEU A 32 SHEET 4 B 5 GLY A 78 GLY A 90 -1 N TYR A 83 O GLY A 180 SHEET 5 B 5 TRP A 141 LEU A 153 -1 O GLN A 143 N PHE A 88 SHEET 1 C 5 ASN A 66 THR A 68 0 SHEET 2 C 5 PHE A 71 LEU A 73 -1 O LEU A 73 N ASN A 66 SHEET 3 C 5 LYS A 158 VAL A 163 -1 O LEU A 159 N LEU A 72 SHEET 4 C 5 SER A 109 THR A 118 -1 N VAL A 117 O LYS A 158 SHEET 5 C 5 TYR A 121 SER A 133 -1 O THR A 125 N LYS A 116 SHEET 1 D 2 THR B 35 ARG B 39 0 SHEET 2 D 2 ARG B 46 ALA B 50 -1 O CYS B 49 N TYR B 36 SHEET 1 E 2 THR B 56 ARG B 60 0 SHEET 2 E 2 THR B 69 PRO B 72 -1 O THR B 69 N ARG B 60 SHEET 1 F 2 HIS B 77 TYR B 78 0 SHEET 2 F 2 ARG B 89 TYR B 90 -1 O ARG B 89 N TYR B 78 SHEET 1 G 2 GLU B 99 ARG B 103 0 SHEET 2 G 2 ALA B 112 CYS B 115 -1 O ARG B 114 N GLU B 100 SHEET 1 H 2 PHE B 119 HIS B 122 0 SHEET 2 H 2 PHE B 125 GLU B 128 -1 O LEU B 127 N PHE B 120 SHEET 1 I 2 ALA B 136 ALA B 140 0 SHEET 2 I 2 GLN B 149 PRO B 152 -1 O GLN B 151 N GLY B 137 SHEET 1 J 2 THR B 157 PHE B 158 0 SHEET 2 J 2 GLN B 169 PRO B 170 -1 O GLN B 169 N PHE B 158 SHEET 1 K 2 LEU B 181 VAL B 183 0 SHEET 2 K 2 LEU B 192 CYS B 193 -1 O LEU B 192 N VAL B 183 SSBOND 1 CYS B 49 CYS B 62 1555 1555 0.87 SSBOND 2 CYS B 52 CYS B 70 1555 1555 2.06 SSBOND 3 CYS B 73 CYS B 88 1555 1555 2.06 SSBOND 4 CYS B 91 CYS B 105 1555 1555 2.05 SSBOND 5 CYS B 95 CYS B 113 1555 1555 1.38 SSBOND 6 CYS B 115 CYS B 126 1555 1555 2.04 SSBOND 7 CYS B 132 CYS B 150 1555 1555 2.03 SSBOND 8 CYS B 153 CYS B 168 1555 1555 2.04 SSBOND 9 CYS B 174 CYS B 193 1555 1555 2.04 CRYST1 74.890 74.890 143.125 90.00 90.00 120.00 P 3 2 1 6 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 0.013353 0.007709 0.000000 0.00000 SCALE2 0.000000 0.015419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006987 0.00000