PDB Short entry for 4KG8 HEADER CYTOKINE 28-APR-13 4KG8 TITLE CRYSTAL STRUCTURE OF LIGHT MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 14; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: HERPES VIRUS ENTRY MEDIATOR LIGAND, HVEM-L, HERPESVIRUS COMPND 5 ENTRY MEDIATOR LIGAND, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY COMPND 6 MEMBER 14, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY COMPND 7 MEMBER 14, SOLUBLE FORM; COMPND 8 ENGINEERED: YES; COMPND 9 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: TNFSF14, HVEML, LIGHT, UNQ391/PRO726; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, NEW YORK STRUCTURAL GENOMICS KEYWDS 2 RESEARCH CONSORTIUM, NYSGRC, IMMUNITY, TNF SUPERFAMILY, HVEM, DCR3, KEYWDS 3 N-GLYCOSYLATION, MEMBRANE, SECRETED PROTEIN, CYTOKINE, ATOMS-TO- KEYWDS 4 ANIMALS: THE IMMUNE FUNCTION NETWORK, JELLY-ROLL FOLD, BIND TNF KEYWDS 5 RECEPTOR HVEM AND LTBR, LTBR, PROTEIN STRUCTURE INITIATIVE, IFN EXPDTA X-RAY DIFFRACTION AUTHOR W.LIU,C.ZHAN,P.R.KUMAR,J.B.BONANNO,S.G.NATHENSON,S.C.ALMO,NEW YORK AUTHOR 2 STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC),ATOMS-TO-ANIMALS: AUTHOR 3 THE IMMUNE FUNCTION NETWORK (IFN) REVDAT 4 20-SEP-23 4KG8 1 REMARK REVDAT 3 31-DEC-14 4KG8 1 JRNL REVDAT 2 18-SEP-13 4KG8 1 AUTHOR REVDAT 1 07-AUG-13 4KG8 0 JRNL AUTH W.LIU,C.ZHAN,H.CHENG,P.R.KUMAR,J.B.BONANNO,S.G.NATHENSON, JRNL AUTH 2 S.C.ALMO JRNL TITL MECHANISTIC BASIS FOR FUNCTIONAL PROMISCUITY IN THE TNF AND JRNL TITL 2 TNF RECEPTOR SUPERFAMILIES: STRUCTURE OF THE LIGHT:DCR3 JRNL TITL 3 ASSEMBLY. JRNL REF STRUCTURE V. 22 1252 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 25087510 JRNL DOI 10.1016/J.STR.2014.06.013 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17608 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 949 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1231 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2818 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.93000 REMARK 3 B22 (A**2) : -1.12000 REMARK 3 B33 (A**2) : 0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.75000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.326 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.316 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2880 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2696 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3901 ; 1.885 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6167 ; 0.852 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 8.455 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;33.888 ;22.984 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 434 ;18.484 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.314 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3221 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 690 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 4KG8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18578 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.44800 REMARK 200 R SYM FOR SHELL (I) : 0.37500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.694 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4EN0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM CITRATE DIBASIC, 20% REMARK 280 (W/V) PEG 3350, PH 5.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.45550 REMARK 290 SMTRY3 2 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: 5090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 LEU A 83 REMARK 465 ILE A 84 REMARK 465 GLN A 85 REMARK 465 GLU A 86 REMARK 465 ARG A 87 REMARK 465 ARG A 88 REMARK 465 SER A 89 REMARK 465 HIS A 90 REMARK 465 GLU A 91 REMARK 465 CYS A 154 REMARK 465 PRO A 155 REMARK 465 LEU A 156 REMARK 465 GLY A 157 REMARK 465 LEU A 158 REMARK 465 ALA A 159 REMARK 465 SER A 160 REMARK 465 CYS A 187 REMARK 465 GLY A 188 REMARK 465 ARG A 189 REMARK 465 ALA A 190 REMARK 465 THR A 191 REMARK 465 SER A 192 REMARK 465 SER A 193 REMARK 465 SER A 194 REMARK 465 VAL A 225 REMARK 465 ARG A 226 REMARK 465 LEU A 227 REMARK 465 ARG A 228 REMARK 465 ASP A 229 REMARK 465 LEU B 83 REMARK 465 ILE B 84 REMARK 465 GLN B 85 REMARK 465 GLU B 86 REMARK 465 ARG B 87 REMARK 465 ARG B 88 REMARK 465 SER B 89 REMARK 465 HIS B 90 REMARK 465 GLU B 91 REMARK 465 VAL B 92 REMARK 465 LEU B 105 REMARK 465 THR B 106 REMARK 465 GLY B 151 REMARK 465 VAL B 152 REMARK 465 GLY B 153 REMARK 465 CYS B 154 REMARK 465 PRO B 155 REMARK 465 LEU B 156 REMARK 465 GLY B 157 REMARK 465 LEU B 158 REMARK 465 PRO B 171 REMARK 465 ARG B 172 REMARK 465 CYS B 187 REMARK 465 GLY B 188 REMARK 465 ARG B 189 REMARK 465 ALA B 190 REMARK 465 THR B 191 REMARK 465 SER B 192 REMARK 465 SER B 193 REMARK 465 SER B 194 REMARK 465 SER B 195 REMARK 465 ARG B 223 REMARK 465 LEU B 224 REMARK 465 VAL B 225 REMARK 465 ARG B 226 REMARK 465 LEU B 227 REMARK 465 ARG B 228 REMARK 465 ASP B 229 REMARK 465 LEU C 83 REMARK 465 ILE C 84 REMARK 465 GLN C 85 REMARK 465 GLU C 86 REMARK 465 ARG C 87 REMARK 465 ARG C 88 REMARK 465 SER C 89 REMARK 465 HIS C 90 REMARK 465 GLU C 91 REMARK 465 VAL C 92 REMARK 465 ALA C 101 REMARK 465 ASN C 102 REMARK 465 SER C 103 REMARK 465 SER C 104 REMARK 465 LEU C 105 REMARK 465 THR C 106 REMARK 465 GLY C 107 REMARK 465 SER C 108 REMARK 465 GLY C 109 REMARK 465 GLY C 153 REMARK 465 CYS C 154 REMARK 465 PRO C 155 REMARK 465 LEU C 156 REMARK 465 GLY C 157 REMARK 465 LEU C 158 REMARK 465 CYS C 187 REMARK 465 GLY C 188 REMARK 465 ARG C 189 REMARK 465 ALA C 190 REMARK 465 THR C 191 REMARK 465 SER C 192 REMARK 465 SER C 193 REMARK 465 SER C 194 REMARK 465 SER C 195 REMARK 465 GLU C 222 REMARK 465 ARG C 223 REMARK 465 LEU C 224 REMARK 465 VAL C 225 REMARK 465 ARG C 226 REMARK 465 LEU C 227 REMARK 465 ARG C 228 REMARK 465 ASP C 229 REMARK 465 GLY C 230 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 OG1 THR B 170 OE2 GLU B 213 2.08 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 124 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 LEU C 118 CA - CB - CG ANGL. DEV. = 18.3 DEGREES REMARK 500 PRO C 186 C - N - CD ANGL. DEV. = -13.5 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 GLN A 117 -38.99 -132.28 REMARK 500 ARG A 223 112.55 -160.47 REMARK 500 GLN B 117 -33.58 -135.00 REMARK 500 THR B 136 -39.24 -132.58 REMARK 500 GLU B 175 -177.21 71.54 REMARK 500 ASP B 221 72.36 59.54 REMARK 500 ARG B 232 38.82 -84.28 REMARK 500 GLN C 117 141.32 -176.06 REMARK 500 ARG C 124 90.27 -162.36 REMARK 500 ASP C 130 62.66 68.84 REMARK 500 SER C 160 32.61 -82.12 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 ALA A 101 ASN A 102 147.27 REMARK 500 GLU A 222 ARG A 223 146.35 REMARK 500 TYR B 173 PRO B 174 33.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EN0 RELATED DB: PDB REMARK 900 RELATED ID: 4J6G RELATED DB: PDB REMARK 900 RELATED ID: 4FHQ RELATED DB: PDB REMARK 900 RELATED ID: 3K51 RELATED DB: PDB REMARK 900 RELATED ID: 3MI8 RELATED DB: PDB REMARK 900 RELATED ID: 3MHD RELATED DB: PDB REMARK 900 RELATED ID: NYSGRC-011104 RELATED DB: TARGETTRACK DBREF 4KG8 A 83 240 UNP O43557 TNF14_HUMAN 83 240 DBREF 4KG8 B 83 240 UNP O43557 TNF14_HUMAN 83 240 DBREF 4KG8 C 83 240 UNP O43557 TNF14_HUMAN 83 240 SEQADV 4KG8 SER A 195 UNP O43557 ARG 195 ENGINEERED MUTATION SEQADV 4KG8 ASN A 196 UNP O43557 VAL 196 ENGINEERED MUTATION SEQADV 4KG8 PHE A 198 UNP O43557 TRP 198 ENGINEERED MUTATION SEQADV 4KG8 GLU A 214 UNP O43557 LYS 214 ENGINEERED MUTATION SEQADV 4KG8 SER B 195 UNP O43557 ARG 195 ENGINEERED MUTATION SEQADV 4KG8 ASN B 196 UNP O43557 VAL 196 ENGINEERED MUTATION SEQADV 4KG8 PHE B 198 UNP O43557 TRP 198 ENGINEERED MUTATION SEQADV 4KG8 GLU B 214 UNP O43557 LYS 214 ENGINEERED MUTATION SEQADV 4KG8 SER C 195 UNP O43557 ARG 195 ENGINEERED MUTATION SEQADV 4KG8 ASN C 196 UNP O43557 VAL 196 ENGINEERED MUTATION SEQADV 4KG8 PHE C 198 UNP O43557 TRP 198 ENGINEERED MUTATION SEQADV 4KG8 GLU C 214 UNP O43557 LYS 214 ENGINEERED MUTATION SEQRES 1 A 158 LEU ILE GLN GLU ARG ARG SER HIS GLU VAL ASN PRO ALA SEQRES 2 A 158 ALA HIS LEU THR GLY ALA ASN SER SER LEU THR GLY SER SEQRES 3 A 158 GLY GLY PRO LEU LEU TRP GLU THR GLN LEU GLY LEU ALA SEQRES 4 A 158 PHE LEU ARG GLY LEU SER TYR HIS ASP GLY ALA LEU VAL SEQRES 5 A 158 VAL THR LYS ALA GLY TYR TYR TYR ILE TYR SER LYS VAL SEQRES 6 A 158 GLN LEU GLY GLY VAL GLY CYS PRO LEU GLY LEU ALA SER SEQRES 7 A 158 THR ILE THR HIS GLY LEU TYR LYS ARG THR PRO ARG TYR SEQRES 8 A 158 PRO GLU GLU LEU GLU LEU LEU VAL SER GLN GLN SER PRO SEQRES 9 A 158 CYS GLY ARG ALA THR SER SER SER SER ASN TRP PHE ASP SEQRES 10 A 158 SER SER PHE LEU GLY GLY VAL VAL HIS LEU GLU ALA GLY SEQRES 11 A 158 GLU GLU VAL VAL VAL ARG VAL LEU ASP GLU ARG LEU VAL SEQRES 12 A 158 ARG LEU ARG ASP GLY THR ARG SER TYR PHE GLY ALA PHE SEQRES 13 A 158 MET VAL SEQRES 1 B 158 LEU ILE GLN GLU ARG ARG SER HIS GLU VAL ASN PRO ALA SEQRES 2 B 158 ALA HIS LEU THR GLY ALA ASN SER SER LEU THR GLY SER SEQRES 3 B 158 GLY GLY PRO LEU LEU TRP GLU THR GLN LEU GLY LEU ALA SEQRES 4 B 158 PHE LEU ARG GLY LEU SER TYR HIS ASP GLY ALA LEU VAL SEQRES 5 B 158 VAL THR LYS ALA GLY TYR TYR TYR ILE TYR SER LYS VAL SEQRES 6 B 158 GLN LEU GLY GLY VAL GLY CYS PRO LEU GLY LEU ALA SER SEQRES 7 B 158 THR ILE THR HIS GLY LEU TYR LYS ARG THR PRO ARG TYR SEQRES 8 B 158 PRO GLU GLU LEU GLU LEU LEU VAL SER GLN GLN SER PRO SEQRES 9 B 158 CYS GLY ARG ALA THR SER SER SER SER ASN TRP PHE ASP SEQRES 10 B 158 SER SER PHE LEU GLY GLY VAL VAL HIS LEU GLU ALA GLY SEQRES 11 B 158 GLU GLU VAL VAL VAL ARG VAL LEU ASP GLU ARG LEU VAL SEQRES 12 B 158 ARG LEU ARG ASP GLY THR ARG SER TYR PHE GLY ALA PHE SEQRES 13 B 158 MET VAL SEQRES 1 C 158 LEU ILE GLN GLU ARG ARG SER HIS GLU VAL ASN PRO ALA SEQRES 2 C 158 ALA HIS LEU THR GLY ALA ASN SER SER LEU THR GLY SER SEQRES 3 C 158 GLY GLY PRO LEU LEU TRP GLU THR GLN LEU GLY LEU ALA SEQRES 4 C 158 PHE LEU ARG GLY LEU SER TYR HIS ASP GLY ALA LEU VAL SEQRES 5 C 158 VAL THR LYS ALA GLY TYR TYR TYR ILE TYR SER LYS VAL SEQRES 6 C 158 GLN LEU GLY GLY VAL GLY CYS PRO LEU GLY LEU ALA SER SEQRES 7 C 158 THR ILE THR HIS GLY LEU TYR LYS ARG THR PRO ARG TYR SEQRES 8 C 158 PRO GLU GLU LEU GLU LEU LEU VAL SER GLN GLN SER PRO SEQRES 9 C 158 CYS GLY ARG ALA THR SER SER SER SER ASN TRP PHE ASP SEQRES 10 C 158 SER SER PHE LEU GLY GLY VAL VAL HIS LEU GLU ALA GLY SEQRES 11 C 158 GLU GLU VAL VAL VAL ARG VAL LEU ASP GLU ARG LEU VAL SEQRES 12 C 158 ARG LEU ARG ASP GLY THR ARG SER TYR PHE GLY ALA PHE SEQRES 13 C 158 MET VAL FORMUL 4 HOH *25(H2 O) SHEET 1 A 3 LEU A 113 GLU A 115 0 SHEET 2 A 3 ALA A 95 ASN A 102 -1 N ASN A 102 O LEU A 113 SHEET 3 A 3 PHE A 122 ARG A 124 -1 O ARG A 124 N ALA A 95 SHEET 1 B 5 LEU A 113 GLU A 115 0 SHEET 2 B 5 ALA A 95 ASN A 102 -1 N ASN A 102 O LEU A 113 SHEET 3 B 5 TYR A 234 MET A 239 -1 O PHE A 235 N LEU A 98 SHEET 4 B 5 GLY A 139 GLY A 151 -1 N LYS A 146 O TYR A 234 SHEET 5 B 5 TRP A 197 LEU A 209 -1 O ASP A 199 N LEU A 149 SHEET 1 C 5 LEU A 126 HIS A 129 0 SHEET 2 C 5 ALA A 132 VAL A 135 -1 O VAL A 134 N SER A 127 SHEET 3 C 5 GLU A 214 LEU A 220 -1 O VAL A 215 N LEU A 133 SHEET 4 C 5 ILE A 162 ARG A 169 -1 N TYR A 167 O VAL A 216 SHEET 5 C 5 LEU A 177 GLN A 184 -1 O GLN A 184 N ILE A 162 SHEET 1 D 3 TRP B 114 GLU B 115 0 SHEET 2 D 3 ALA B 95 GLY B 100 -1 N THR B 99 O GLU B 115 SHEET 3 D 3 PHE B 122 ARG B 124 -1 O ARG B 124 N ALA B 95 SHEET 1 E 5 TRP B 114 GLU B 115 0 SHEET 2 E 5 ALA B 95 GLY B 100 -1 N THR B 99 O GLU B 115 SHEET 3 E 5 TYR B 234 MET B 239 -1 O PHE B 235 N LEU B 98 SHEET 4 E 5 GLY B 139 LEU B 149 -1 N TYR B 142 O PHE B 238 SHEET 5 E 5 ASP B 199 LEU B 209 -1 O LEU B 209 N GLY B 139 SHEET 1 F 5 SER B 127 HIS B 129 0 SHEET 2 F 5 ALA B 132 VAL B 134 -1 O VAL B 134 N SER B 127 SHEET 3 F 5 GLU B 214 VAL B 219 -1 O VAL B 215 N LEU B 133 SHEET 4 F 5 ILE B 162 ARG B 169 -1 N TYR B 167 O VAL B 216 SHEET 5 F 5 LEU B 177 GLN B 184 -1 O LEU B 180 N LEU B 166 SHEET 1 G 5 PHE C 122 ARG C 124 0 SHEET 2 G 5 ALA C 95 THR C 99 -1 N ALA C 95 O ARG C 124 SHEET 3 G 5 TYR C 234 MET C 239 -1 O PHE C 235 N LEU C 98 SHEET 4 G 5 GLY C 139 GLY C 150 -1 N TYR C 144 O GLY C 236 SHEET 5 G 5 PHE C 198 LEU C 209 -1 O SER C 201 N VAL C 147 SHEET 1 H 5 LEU C 126 HIS C 129 0 SHEET 2 H 5 ALA C 132 VAL C 135 -1 O VAL C 134 N SER C 127 SHEET 3 H 5 GLU C 214 LEU C 220 -1 O VAL C 215 N LEU C 133 SHEET 4 H 5 ILE C 162 ARG C 169 -1 N GLY C 165 O ARG C 218 SHEET 5 H 5 LEU C 177 GLN C 184 -1 O GLN C 184 N ILE C 162 CISPEP 1 LEU A 220 ASP A 221 0 -0.06 CISPEP 2 ARG A 223 LEU A 224 0 -5.47 CISPEP 3 SER B 103 SER B 104 0 13.61 CISPEP 4 GLY B 107 SER B 108 0 15.21 CISPEP 5 GLY B 109 GLY B 110 0 -0.26 CISPEP 6 GLN C 117 LEU C 118 0 -4.44 CISPEP 7 LEU C 118 GLY C 119 0 3.00 CISPEP 8 ASN C 196 TRP C 197 0 -15.79 CRYST1 59.644 46.911 70.400 90.00 98.02 90.00 P 1 21 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 0.016766 0.000000 0.002363 0.00000 SCALE2 0.000000 0.021317 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014345 0.00000