HEADER STRUCTURAL PROTEIN/IMMUNE SYSTEM 30-NOV-17 6BRB TITLE NOVEL NON-ANTIBODY PROTEIN SCAFFOLD TARGETING CD40L COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD40 LIGAND; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 120-261; COMPND 5 SYNONYM: CD40-L, T-CELL ANTIGEN GP39, TNF-RELATED ACTIVATION PROTEIN, COMPND 6 TRAP, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 5; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TN3-LIKE; COMPND 10 CHAIN: D; COMPND 11 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: CD40LG, CD40L, TNFSF5, TRAP; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 11 ORGANISM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TN3 RELATED, TNF LIGAND RELATED, STRUCTURAL PROTEIN-IMMUNE SYSTEM KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.OGANESYAN,M.BACA,T.THISTED,L.GRINBERG,H.WU,W.F.DALL'ACQUA REVDAT 4 04-OCT-23 6BRB 1 HETSYN REVDAT 3 29-JUL-20 6BRB 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 19-JUN-19 6BRB 1 JRNL REVDAT 1 05-DEC-18 6BRB 0 JRNL AUTH J.L.KARNELL,M.ALBULESCU,S.DRABIC,L.WANG,R.MOATE,M.BACA, JRNL AUTH 2 V.OGANESYAN,M.GUNSIOR,T.THISTED,L.YAN,J.LI,X.XIONG,S.C.ECK, JRNL AUTH 3 M.DE LOS REYES,I.YUSUF,K.STREICHER,U.MULLER-LADNER,D.HOWE, JRNL AUTH 4 R.ETTINGER,R.HERBST,J.DRAPPA JRNL TITL A CD40L-TARGETING PROTEIN REDUCES AUTOANTIBODIES AND JRNL TITL 2 IMPROVES DISEASE ACTIVITY IN PATIENTS WITH AUTOIMMUNITY. JRNL REF SCI TRANSL MED V. 11 2019 JRNL REFN ESSN 1946-6242 JRNL PMID 31019027 JRNL DOI 10.1126/SCITRANSLMED.AAR6584 REMARK 2 REMARK 2 RESOLUTION. 2.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 7531 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 829 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) : 2.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 546 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1779 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 26.53000 REMARK 3 B22 (A**2) : 26.53000 REMARK 3 B33 (A**2) : -53.05000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.425 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.250 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.709 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1864 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1669 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2540 ; 1.271 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3886 ; 0.824 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 227 ; 7.346 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;36.585 ;24.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 294 ;15.407 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 9.995 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 295 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2041 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 376 ; 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): 914 ; 0.727 ; 3.904 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 913 ; 0.728 ; 3.904 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1139 ; 1.271 ; 5.856 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1140 ; 1.270 ; 5.855 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 950 ; 0.674 ; 4.078 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 951 ; 0.674 ; 4.077 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1402 ; 1.193 ; 6.086 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1881 ; 2.372 ;44.350 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1881 ; 2.359 ;44.348 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 : 7 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 120 A 173 REMARK 3 ORIGIN FOR THE GROUP (A): -37.9907 13.8183 -36.0439 REMARK 3 T TENSOR REMARK 3 T11: 0.1393 T22: 0.0372 REMARK 3 T33: 0.0822 T12: 0.0251 REMARK 3 T13: 0.0268 T23: -0.0360 REMARK 3 L TENSOR REMARK 3 L11: 1.7967 L22: 5.6594 REMARK 3 L33: 5.3876 L12: 0.4251 REMARK 3 L13: -0.0973 L23: -0.5344 REMARK 3 S TENSOR REMARK 3 S11: -0.1840 S12: 0.0103 S13: -0.2639 REMARK 3 S21: -0.4204 S22: 0.1847 S23: -0.4610 REMARK 3 S31: 0.4399 S32: 0.0859 S33: -0.0008 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 : A 174 A 203 REMARK 3 ORIGIN FOR THE GROUP (A): -33.1155 21.4437 -21.9645 REMARK 3 T TENSOR REMARK 3 T11: 0.1377 T22: 0.0717 REMARK 3 T33: 0.1008 T12: 0.0184 REMARK 3 T13: -0.0501 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 3.9388 L22: 1.9460 REMARK 3 L33: 8.8636 L12: 0.8782 REMARK 3 L13: -2.7815 L23: -1.3109 REMARK 3 S TENSOR REMARK 3 S11: -0.1662 S12: -0.0477 S13: 0.0082 REMARK 3 S21: 0.0777 S22: -0.0844 S23: -0.2167 REMARK 3 S31: -0.0830 S32: 0.6363 S33: 0.2505 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 : A 204 A 261 REMARK 3 ORIGIN FOR THE GROUP (A): -39.0271 20.6151 -25.6591 REMARK 3 T TENSOR REMARK 3 T11: 0.0217 T22: 0.0254 REMARK 3 T33: 0.0182 T12: 0.0093 REMARK 3 T13: -0.0153 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.6248 L22: 3.2600 REMARK 3 L33: 3.1512 L12: 0.6200 REMARK 3 L13: 0.2586 L23: -0.1536 REMARK 3 S TENSOR REMARK 3 S11: -0.0526 S12: -0.0991 S13: 0.0377 REMARK 3 S21: 0.0562 S22: 0.0065 S23: -0.1803 REMARK 3 S31: -0.1054 S32: 0.1695 S33: 0.0461 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 17 REMARK 3 ORIGIN FOR THE GROUP (A): -39.5221 -2.0968 -17.3390 REMARK 3 T TENSOR REMARK 3 T11: 0.2856 T22: 0.0885 REMARK 3 T33: 0.1145 T12: 0.0396 REMARK 3 T13: -0.0138 T23: -0.0908 REMARK 3 L TENSOR REMARK 3 L11: 3.9223 L22: 11.8904 REMARK 3 L33: 9.4971 L12: -4.8075 REMARK 3 L13: -3.5991 L23: -1.6736 REMARK 3 S TENSOR REMARK 3 S11: 0.3477 S12: 0.3277 S13: -0.2916 REMARK 3 S21: -0.7209 S22: -0.3498 S23: 0.6176 REMARK 3 S31: 0.0801 S32: -0.2959 S33: 0.0021 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 18 D 25 REMARK 3 ORIGIN FOR THE GROUP (A): -55.6896 6.8236 -14.8498 REMARK 3 T TENSOR REMARK 3 T11: 0.2037 T22: 0.3425 REMARK 3 T33: 0.4032 T12: 0.0109 REMARK 3 T13: -0.0392 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 3.1765 L22: 12.3460 REMARK 3 L33: 7.2815 L12: 3.9322 REMARK 3 L13: 1.8735 L23: 8.9764 REMARK 3 S TENSOR REMARK 3 S11: 0.1863 S12: 0.3849 S13: -0.3309 REMARK 3 S21: 0.2606 S22: -0.6647 S23: 0.6169 REMARK 3 S31: 0.1765 S32: -0.9602 S33: 0.4784 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 26 D 68 REMARK 3 ORIGIN FOR THE GROUP (A): -42.2119 -2.1025 -8.1035 REMARK 3 T TENSOR REMARK 3 T11: 0.2279 T22: 0.0692 REMARK 3 T33: 0.0782 T12: -0.0522 REMARK 3 T13: 0.0377 T23: 0.0213 REMARK 3 L TENSOR REMARK 3 L11: 3.9639 L22: 6.5636 REMARK 3 L33: 3.3982 L12: -3.4797 REMARK 3 L13: 1.6249 L23: -0.7381 REMARK 3 S TENSOR REMARK 3 S11: -0.1036 S12: -0.3325 S13: -0.4713 REMARK 3 S21: 0.2759 S22: 0.2741 S23: 0.2988 REMARK 3 S31: 0.3216 S32: -0.0391 S33: -0.1705 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 69 D 87 REMARK 3 ORIGIN FOR THE GROUP (A): -47.8209 -3.7899 -10.8091 REMARK 3 T TENSOR REMARK 3 T11: 0.2976 T22: 0.2686 REMARK 3 T33: 0.2476 T12: -0.1033 REMARK 3 T13: 0.0745 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 9.1881 L22: 6.1584 REMARK 3 L33: 3.7096 L12: -3.5303 REMARK 3 L13: 0.6917 L23: 1.7286 REMARK 3 S TENSOR REMARK 3 S11: -0.5534 S12: 0.5604 S13: -0.6148 REMARK 3 S21: 0.5396 S22: -0.0014 S23: 0.9934 REMARK 3 S31: 0.2225 S32: -0.5102 S33: 0.5548 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 6BRB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1000231179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.820 REMARK 200 RESOLUTION RANGE LOW (A) : 51.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.19500 REMARK 200 R SYM (I) : 0.19500 REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.79600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRIES 1ALY & 1TEN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% V/V PEG600, 0.1 M SODIUM ACETATE, REMARK 280 0.2 M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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: 13000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 -46.76400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 80.99762 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -93.52800 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 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 A 217 C - N - CD ANGL. DEV. = -16.8 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 HIS A 125 116.74 -162.82 REMARK 500 SER A 132 41.80 -91.49 REMARK 500 THR A 134 -46.84 69.99 REMARK 500 TYR A 145 56.58 -96.81 REMARK 500 ASN A 157 27.85 49.20 REMARK 500 GLN A 186 78.63 -66.77 REMARK 500 PRO A 217 -65.73 21.98 REMARK 500 ILE D 2 85.66 -164.76 REMARK 500 THR D 8 -155.25 -129.89 REMARK 500 ALA D 12 139.20 -172.53 REMARK 500 ASP D 18 43.37 -93.12 REMARK 500 GLU D 22 47.94 -93.03 REMARK 500 VAL D 24 -66.13 -123.94 REMARK 500 PRO D 77 109.67 -56.77 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 LYS A 216 PRO A 217 -131.80 REMARK 500 REMARK 500 REMARK: NULL DBREF 6BRB A 120 261 UNP P29965 CD40L_HUMAN 120 261 DBREF 6BRB D 1 87 PDB 6BRB 6BRB 1 87 SEQRES 1 A 142 PRO GLN ILE ALA ALA HIS VAL ILE SER GLU ALA SER SER SEQRES 2 A 142 LYS THR THR SER VAL LEU GLN TRP ALA GLU LYS GLY TYR SEQRES 3 A 142 TYR THR MET SER ASN ASN LEU VAL THR LEU GLU ASN GLY SEQRES 4 A 142 LYS GLN LEU THR VAL LYS ARG GLN GLY LEU TYR TYR ILE SEQRES 5 A 142 TYR ALA GLN VAL THR PHE CYS SER ASN ARG GLU ALA SER SEQRES 6 A 142 SER GLN ALA PRO PHE ILE ALA SER LEU CYS LEU LYS SER SEQRES 7 A 142 PRO GLY ARG PHE GLU ARG ILE LEU LEU ARG ALA ALA ASN SEQRES 8 A 142 THR HIS SER SER ALA LYS PRO CYS GLY GLN GLN SER ILE SEQRES 9 A 142 HIS LEU GLY GLY VAL PHE GLU LEU GLN PRO GLY ALA SER SEQRES 10 A 142 VAL PHE VAL ASN VAL THR ASP PRO SER GLN VAL SER HIS SEQRES 11 A 142 GLY THR GLY PHE THR SER PHE GLY LEU LEU LYS LEU SEQRES 1 D 87 ALA ILE GLU VAL LYS ASP VAL THR ASP THR THR ALA LEU SEQRES 2 D 87 ILE THR TRP SER ASP ASP PHE GLY GLU TYR VAL TRP CYS SEQRES 3 D 87 GLU LEU THR TYR GLY ILE LYS ASP VAL PRO GLY ASP ARG SEQRES 4 D 87 THR THR ILE ASP LEU TRP TYR HIS HIS ALA HIS TYR SER SEQRES 5 D 87 ILE GLY ASN LEU LYS PRO ASP THR GLU TYR GLU VAL SER SEQRES 6 D 87 LEU ILE CYS ARG ARG GLY ASP MET SER SER ASN PRO ALA SEQRES 7 D 87 LYS GLU THR PHE THR THR GLY LEU VAL HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 3 BMA C6 H12 O6 FORMUL 4 HOH *17(H2 O) HELIX 1 AA1 ASP A 243 VAL A 247 5 5 SHEET 1 AA1 3 TRP A 140 ALA A 141 0 SHEET 2 AA1 3 ALA A 123 SER A 128 -1 N ILE A 127 O ALA A 141 SHEET 3 AA1 3 THR A 147 MET A 148 -1 O THR A 147 N HIS A 125 SHEET 1 AA2 5 TRP A 140 ALA A 141 0 SHEET 2 AA2 5 ALA A 123 SER A 128 -1 N ILE A 127 O ALA A 141 SHEET 3 AA2 5 SER A 255 LYS A 260 -1 O PHE A 256 N VAL A 126 SHEET 4 AA2 5 GLY A 167 SER A 179 -1 N TYR A 170 O LEU A 259 SHEET 5 AA2 5 GLY A 219 LEU A 231 -1 O ILE A 223 N VAL A 175 SHEET 1 AA3 5 VAL A 153 GLU A 156 0 SHEET 2 AA3 5 GLN A 160 VAL A 163 -1 O GLN A 160 N GLU A 156 SHEET 3 AA3 5 SER A 236 VAL A 241 -1 O VAL A 237 N LEU A 161 SHEET 4 AA3 5 PHE A 189 LYS A 196 -1 N CYS A 194 O PHE A 238 SHEET 5 AA3 5 GLU A 202 ASN A 210 -1 O ASN A 210 N PHE A 189 SHEET 1 AA4 3 ILE D 2 LYS D 5 0 SHEET 2 AA4 3 ALA D 12 TRP D 16 -1 O LEU D 13 N LYS D 5 SHEET 3 AA4 3 HIS D 50 ILE D 53 -1 O TYR D 51 N ILE D 14 SHEET 1 AA5 4 ARG D 39 TRP D 45 0 SHEET 2 AA5 4 TRP D 25 ILE D 32 -1 N LEU D 28 O ILE D 42 SHEET 3 AA5 4 GLU D 61 ARG D 70 -1 O ARG D 69 N TRP D 25 SHEET 4 AA5 4 MET D 73 SER D 74 -1 O MET D 73 N ARG D 70 SHEET 1 AA6 4 ARG D 39 TRP D 45 0 SHEET 2 AA6 4 TRP D 25 ILE D 32 -1 N LEU D 28 O ILE D 42 SHEET 3 AA6 4 GLU D 61 ARG D 70 -1 O ARG D 69 N TRP D 25 SHEET 4 AA6 4 ALA D 78 THR D 83 -1 O GLU D 80 N VAL D 64 SSBOND 1 CYS A 178 CYS A 218 1555 1555 2.05 SSBOND 2 CYS D 26 CYS D 68 1555 1555 2.06 LINK ND2 ASN A 240 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 CRYST1 93.528 93.528 66.685 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 0.010692 0.006173 0.000000 0.00000 SCALE2 0.000000 0.012346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014996 0.00000