HEADER SIGNALING PROTEIN 15-FEB-23 8CKK TITLE SEMAPHORIN-5A TSR 3-4 DOMAINS IN COMPLEX WITH NITRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEMAPHORIN-5A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SEMAPHORIN-F,SEMA F; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: N-TERMINAL 'ET' PEPTIDE AND C-TERMINAL 'GTLEVLFQ' COMPND 7 PEPTIDES ARE RECOMBINANT ADDITIONS ENCODED BY THE EXPRESSION VECTOR. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SEMA5A, SEMAF; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 9 EXPRESSION_SYSTEM_ATCC_NUMBER: CRL-3216; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PHL-SEC KEYWDS SEMAPHORIN, CELL SIGNALLING, AXON GUIDANCE CUE, GLYCOSAMINOGLYCAN KEYWDS 2 BINDING PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.N.NAGY,R.DUMAN,K.HARLOS,K.EL OMARI,A.WAGNER,E.Y.JONES REVDAT 1 28-FEB-24 8CKK 0 JRNL AUTH G.N.NAGY,R.DUMAN,K.HARLOS,K.EL OMARI,A.WAGNER,E.Y.JONES JRNL TITL SEMAPHORIN-5A TSR 3-4 DOMAINS IN COMPLEX WITH NITRATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 55.8 REMARK 3 NUMBER OF REFLECTIONS : 24526 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.7500 - 3.2400 1.00 4925 250 0.1669 0.1914 REMARK 3 2 3.2400 - 2.5700 1.00 4717 261 0.2023 0.2428 REMARK 3 3 2.5700 - 2.2500 0.99 4639 216 0.2275 0.2709 REMARK 3 4 2.2500 - 2.0400 0.84 3897 209 0.2269 0.2763 REMARK 3 5 2.0400 - 1.8900 0.52 2427 111 0.2388 0.2583 REMARK 3 6 1.8900 - 1.7800 0.30 1406 73 0.2585 0.2668 REMARK 3 7 1.7800 - 1.6900 0.18 814 47 0.2842 0.3124 REMARK 3 8 1.6900 - 1.6200 0.08 365 20 0.3228 0.3836 REMARK 3 9 1.6200 - 1.5600 0.03 144 7 0.3437 0.5894 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.198 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.574 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1967 REMARK 3 ANGLE : 0.629 2660 REMARK 3 CHIRALITY : 0.041 271 REMARK 3 PLANARITY : 0.004 356 REMARK 3 DIHEDRAL : 10.273 711 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 651 THROUGH 677 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6856 36.5972 65.1144 REMARK 3 T TENSOR REMARK 3 T11: 0.2357 T22: 0.1347 REMARK 3 T33: 0.1426 T12: -0.0371 REMARK 3 T13: -0.0653 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.2242 L22: 4.0710 REMARK 3 L33: 2.9132 L12: -1.0509 REMARK 3 L13: 0.0921 L23: -2.8550 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: 0.0934 S13: 0.0765 REMARK 3 S21: -0.4163 S22: 0.1129 S23: 0.1494 REMARK 3 S31: 0.1784 S32: -0.0451 S33: -0.0625 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 678 THROUGH 712 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.9054 25.2586 70.5964 REMARK 3 T TENSOR REMARK 3 T11: 0.2486 T22: 0.1812 REMARK 3 T33: 0.1180 T12: -0.0475 REMARK 3 T13: -0.0989 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 0.1524 L22: 9.2217 REMARK 3 L33: 0.1638 L12: 0.4781 REMARK 3 L13: -0.5642 L23: -2.1855 REMARK 3 S TENSOR REMARK 3 S11: 0.0353 S12: -0.0035 S13: 0.0297 REMARK 3 S21: 0.1487 S22: -0.0483 S23: 0.1168 REMARK 3 S31: -0.0886 S32: 0.0445 S33: 0.0106 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 713 THROUGH 722 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5473 -25.5343 88.3112 REMARK 3 T TENSOR REMARK 3 T11: 0.3527 T22: 0.4087 REMARK 3 T33: 0.5127 T12: -0.0075 REMARK 3 T13: 0.1187 T23: 0.3037 REMARK 3 L TENSOR REMARK 3 L11: 0.9971 L22: 5.1337 REMARK 3 L33: 7.6026 L12: 2.1569 REMARK 3 L13: -0.3276 L23: 1.3015 REMARK 3 S TENSOR REMARK 3 S11: -0.2133 S12: -1.7650 S13: -1.2497 REMARK 3 S21: 0.9107 S22: -0.1283 S23: -0.3443 REMARK 3 S31: 1.4388 S32: -0.0426 S33: 0.2330 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 723 THROUGH 742 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8115 -4.8712 80.1468 REMARK 3 T TENSOR REMARK 3 T11: 0.1234 T22: 0.1536 REMARK 3 T33: 0.1294 T12: 0.0164 REMARK 3 T13: 0.0035 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.3198 L22: 7.0553 REMARK 3 L33: 2.6796 L12: 2.1497 REMARK 3 L13: -0.7170 L23: -3.2469 REMARK 3 S TENSOR REMARK 3 S11: -0.0702 S12: -0.0344 S13: -0.1769 REMARK 3 S21: -0.0392 S22: -0.1471 S23: -0.3459 REMARK 3 S31: -0.1793 S32: -0.0290 S33: 0.1871 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 743 THROUGH 763 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7781 -15.1873 87.2988 REMARK 3 T TENSOR REMARK 3 T11: 0.1214 T22: 0.2145 REMARK 3 T33: 0.2134 T12: -0.0366 REMARK 3 T13: -0.0527 T23: 0.0721 REMARK 3 L TENSOR REMARK 3 L11: 4.4815 L22: 7.0128 REMARK 3 L33: 2.0517 L12: -3.2308 REMARK 3 L13: 1.3124 L23: -0.6641 REMARK 3 S TENSOR REMARK 3 S11: 0.1273 S12: -0.4183 S13: -0.2355 REMARK 3 S21: 0.2769 S22: -0.1515 S23: -0.3565 REMARK 3 S31: 0.4515 S32: 0.2775 S33: 0.1099 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 652 THROUGH 677 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4448 39.2225 75.5410 REMARK 3 T TENSOR REMARK 3 T11: 0.2133 T22: 0.1649 REMARK 3 T33: 0.2487 T12: 0.0081 REMARK 3 T13: -0.0970 T23: -0.0239 REMARK 3 L TENSOR REMARK 3 L11: 1.9335 L22: 8.7839 REMARK 3 L33: 1.7167 L12: 1.6317 REMARK 3 L13: -0.6264 L23: 0.1098 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: -0.0115 S13: -0.1642 REMARK 3 S21: 0.5890 S22: 0.2531 S23: -0.8641 REMARK 3 S31: 0.1741 S32: 0.0830 S33: -0.1785 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 678 THROUGH 696 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9087 45.8169 72.8133 REMARK 3 T TENSOR REMARK 3 T11: 0.2142 T22: 0.2167 REMARK 3 T33: 0.2642 T12: -0.0246 REMARK 3 T13: -0.0688 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.2690 L22: 3.4960 REMARK 3 L33: 1.2155 L12: 0.5933 REMARK 3 L13: -0.3616 L23: 0.3013 REMARK 3 S TENSOR REMARK 3 S11: -0.0306 S12: 0.1152 S13: -0.0379 REMARK 3 S21: -0.3196 S22: 0.1097 S23: 0.1732 REMARK 3 S31: 0.0532 S32: -0.1211 S33: -0.0420 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 697 THROUGH 712 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6068 4.8890 81.0183 REMARK 3 T TENSOR REMARK 3 T11: 0.2186 T22: 0.1641 REMARK 3 T33: 0.2895 T12: 0.0176 REMARK 3 T13: -0.0210 T23: 0.0217 REMARK 3 L TENSOR REMARK 3 L11: 1.3228 L22: 3.4889 REMARK 3 L33: 1.6507 L12: -0.0658 REMARK 3 L13: -0.5688 L23: -0.7374 REMARK 3 S TENSOR REMARK 3 S11: -0.2297 S12: -0.2029 S13: 0.3354 REMARK 3 S21: -0.5542 S22: 0.2624 S23: -0.5308 REMARK 3 S31: -0.1108 S32: -0.0699 S33: -0.0157 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 713 THROUGH 722 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.5378 -25.8037 89.2502 REMARK 3 T TENSOR REMARK 3 T11: 0.5842 T22: 0.3915 REMARK 3 T33: 0.5850 T12: 0.0209 REMARK 3 T13: -0.1101 T23: 0.2192 REMARK 3 L TENSOR REMARK 3 L11: 6.3611 L22: 0.0518 REMARK 3 L33: 6.0505 L12: 0.2206 REMARK 3 L13: -0.1816 L23: -0.5164 REMARK 3 S TENSOR REMARK 3 S11: 0.1800 S12: 0.5250 S13: -1.4045 REMARK 3 S21: -0.3359 S22: -0.0517 S23: -0.0508 REMARK 3 S31: 1.9730 S32: -0.3737 S33: 0.1580 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 723 THROUGH 742 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4027 -4.6563 83.9920 REMARK 3 T TENSOR REMARK 3 T11: 0.1612 T22: 0.1780 REMARK 3 T33: 0.2143 T12: -0.0098 REMARK 3 T13: -0.0174 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 1.5911 L22: 3.0376 REMARK 3 L33: 1.5772 L12: -0.8704 REMARK 3 L13: 0.5885 L23: -0.5160 REMARK 3 S TENSOR REMARK 3 S11: -0.0693 S12: -0.1817 S13: 0.1050 REMARK 3 S21: 0.2238 S22: 0.0554 S23: -0.2757 REMARK 3 S31: -0.2842 S32: -0.0534 S33: 0.0446 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 743 THROUGH 752 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5744 -5.4879 85.0886 REMARK 3 T TENSOR REMARK 3 T11: 0.1940 T22: 0.1915 REMARK 3 T33: 0.2233 T12: 0.0398 REMARK 3 T13: 0.1033 T23: 0.0378 REMARK 3 L TENSOR REMARK 3 L11: 2.2412 L22: 3.0582 REMARK 3 L33: 0.6885 L12: 1.9069 REMARK 3 L13: 0.6797 L23: 0.0670 REMARK 3 S TENSOR REMARK 3 S11: 0.1275 S12: -0.1416 S13: 0.3216 REMARK 3 S21: 0.6540 S22: -0.0772 S23: 0.5300 REMARK 3 S31: -0.1782 S32: -0.0227 S33: -0.0256 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 753 THROUGH 772 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5519 -31.4383 81.0865 REMARK 3 T TENSOR REMARK 3 T11: 0.4719 T22: 0.3006 REMARK 3 T33: 0.2169 T12: 0.0244 REMARK 3 T13: -0.0914 T23: -0.0649 REMARK 3 L TENSOR REMARK 3 L11: 3.5182 L22: 8.6404 REMARK 3 L33: 1.7375 L12: -1.2674 REMARK 3 L13: -2.3505 L23: 1.0924 REMARK 3 S TENSOR REMARK 3 S11: 0.1409 S12: 0.3259 S13: -0.3745 REMARK 3 S21: -0.5787 S22: 0.0814 S23: 0.9337 REMARK 3 S31: 1.0686 S32: 0.0236 S33: -0.1451 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8CKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292127724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24530 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.557 REMARK 200 RESOLUTION RANGE LOW (A) : 53.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 55.4 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 8.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : 1.56400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, 6 M AMMONIUM REMARK 280 NITRATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, 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 25.94700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.75100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.17350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.75100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.94700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.17350 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: DIMERIC 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 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 GLU A 649 REMARK 465 THR A 650 REMARK 465 SER A 764 REMARK 465 THR A 765 REMARK 465 GLY A 766 REMARK 465 THR A 767 REMARK 465 LEU A 768 REMARK 465 GLU A 769 REMARK 465 VAL A 770 REMARK 465 LEU A 771 REMARK 465 PHE A 772 REMARK 465 GLN A 773 REMARK 465 GLU B 649 REMARK 465 THR B 650 REMARK 465 GLY B 651 REMARK 465 GLN B 773 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 ASP A 720 CG OD1 OD2 REMARK 470 ASN A 721 CG OD1 ND2 REMARK 470 ARG B 664 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 721 CG OD1 ND2 REMARK 470 ARG B 736 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 744 CG CD OE1 OE2 REMARK 470 SER B 757 OG REMARK 470 ASP B 758 CG OD1 OD2 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 685 52.87 -100.94 REMARK 500 ASP B 685 67.16 -108.73 REMARK 500 ASP B 758 56.71 -98.53 REMARK 500 THR B 765 -61.26 -144.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CKK A 652 765 UNP Q13591 SEM5A_HUMAN 652 765 DBREF 8CKK B 652 765 UNP Q13591 SEM5A_HUMAN 652 765 SEQADV 8CKK GLU A 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKK THR A 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLY A 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLY A 766 UNP Q13591 EXPRESSION TAG SEQADV 8CKK THR A 767 UNP Q13591 EXPRESSION TAG SEQADV 8CKK LEU A 768 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLU A 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKK VAL A 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKK LEU A 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKK PHE A 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLN A 773 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLU B 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKK THR B 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLY B 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLY B 766 UNP Q13591 EXPRESSION TAG SEQADV 8CKK THR B 767 UNP Q13591 EXPRESSION TAG SEQADV 8CKK LEU B 768 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLU B 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKK VAL B 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKK LEU B 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKK PHE B 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKK GLN B 773 UNP Q13591 EXPRESSION TAG SEQRES 1 A 125 GLU THR GLY PRO HIS MET PHE TRP THR GLY TRP GLY PRO SEQRES 2 A 125 TRP GLU ARG CYS THR ALA GLN CYS GLY GLY GLY ILE GLN SEQRES 3 A 125 ALA ARG ARG ARG ILE CYS GLU ASN GLY PRO ASP CYS ALA SEQRES 4 A 125 GLY CYS ASN VAL GLU TYR GLN SER CYS ASN THR ASN PRO SEQRES 5 A 125 CYS PRO GLU LEU LYS LYS THR THR PRO TRP THR PRO TRP SEQRES 6 A 125 THR PRO VAL ASN ILE SER ASP ASN GLY GLY HIS TYR GLU SEQRES 7 A 125 GLN ARG PHE ARG TYR THR CYS LYS ALA ARG LEU ALA ASP SEQRES 8 A 125 PRO ASN LEU LEU GLU VAL GLY ARG GLN ARG ILE GLU MET SEQRES 9 A 125 ARG TYR CYS SER SER ASP GLY THR SER GLY CYS SER THR SEQRES 10 A 125 GLY THR LEU GLU VAL LEU PHE GLN SEQRES 1 B 125 GLU THR GLY PRO HIS MET PHE TRP THR GLY TRP GLY PRO SEQRES 2 B 125 TRP GLU ARG CYS THR ALA GLN CYS GLY GLY GLY ILE GLN SEQRES 3 B 125 ALA ARG ARG ARG ILE CYS GLU ASN GLY PRO ASP CYS ALA SEQRES 4 B 125 GLY CYS ASN VAL GLU TYR GLN SER CYS ASN THR ASN PRO SEQRES 5 B 125 CYS PRO GLU LEU LYS LYS THR THR PRO TRP THR PRO TRP SEQRES 6 B 125 THR PRO VAL ASN ILE SER ASP ASN GLY GLY HIS TYR GLU SEQRES 7 B 125 GLN ARG PHE ARG TYR THR CYS LYS ALA ARG LEU ALA ASP SEQRES 8 B 125 PRO ASN LEU LEU GLU VAL GLY ARG GLN ARG ILE GLU MET SEQRES 9 B 125 ARG TYR CYS SER SER ASP GLY THR SER GLY CYS SER THR SEQRES 10 B 125 GLY THR LEU GLU VAL LEU PHE GLN HET MAN A 801 11 HET NO3 A 802 4 HET NO3 A 803 4 HET NO3 A 804 4 HET NO3 A 805 4 HET NO3 A 806 4 HET NO3 A 807 4 HET NO3 A 808 4 HET NO3 A 809 4 HET NO3 A 810 4 HET MAN A 811 11 HET NO3 B 801 4 HET NO3 B 802 4 HET NO3 B 803 4 HET NO3 B 804 4 HET NO3 B 805 4 HET NO3 B 806 4 HET NO3 B 807 4 HET NO3 B 808 4 HET MAN B 809 11 HET MAN B 810 11 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM NO3 NITRATE ION HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 MAN 4(C6 H12 O6) FORMUL 4 NO3 17(N O3 1-) FORMUL 24 HOH *169(H2 O) HELIX 1 AA1 ASP A 739 ASN A 741 5 3 HELIX 2 AA2 ASP B 739 ASN B 741 5 3 HELIX 3 AA3 GLY B 766 PHE B 772 5 7 SHEET 1 AA1 2 PHE A 655 TRP A 656 0 SHEET 2 AA1 2 CYS A 680 GLU A 681 -1 O GLU A 681 N PHE A 655 SHEET 1 AA2 2 GLY A 672 ARG A 677 0 SHEET 2 AA2 2 VAL A 691 CYS A 696 -1 O CYS A 696 N GLY A 672 SHEET 1 AA3 3 GLU A 703 THR A 707 0 SHEET 2 AA3 3 THR A 732 ARG A 736 -1 O CYS A 733 N LYS A 706 SHEET 3 AA3 3 LEU B 743 VAL B 745 -1 O GLU B 744 N LYS A 734 SHEET 1 AA4 3 THR A 714 PRO A 715 0 SHEET 2 AA4 3 HIS A 724 ARG A 730 -1 O GLN A 727 N THR A 714 SHEET 3 AA4 3 ARG B 749 CYS B 755 -1 O CYS B 755 N HIS A 724 SHEET 1 AA5 3 LEU A 743 VAL A 745 0 SHEET 2 AA5 3 THR B 732 ARG B 736 -1 O LYS B 734 N GLU A 744 SHEET 3 AA5 3 GLU B 703 THR B 707 -1 N LYS B 706 O CYS B 733 SHEET 1 AA6 3 ARG A 749 CYS A 755 0 SHEET 2 AA6 3 HIS B 724 ARG B 730 -1 O ARG B 730 N ARG A 749 SHEET 3 AA6 3 THR B 714 PRO B 715 -1 N THR B 714 O GLN B 727 SHEET 1 AA7 2 PHE B 655 TRP B 656 0 SHEET 2 AA7 2 CYS B 680 GLU B 681 -1 O GLU B 681 N PHE B 655 SHEET 1 AA8 2 GLY B 672 ARG B 677 0 SHEET 2 AA8 2 VAL B 691 CYS B 696 -1 O GLN B 694 N GLN B 674 SSBOND 1 CYS A 665 CYS A 696 1555 1555 2.03 SSBOND 2 CYS A 669 CYS A 701 1555 1555 2.04 SSBOND 3 CYS A 680 CYS A 686 1555 1555 2.03 SSBOND 4 CYS A 689 CYS B 689 1555 1555 2.03 SSBOND 5 CYS A 733 CYS B 733 1555 1555 2.03 SSBOND 6 CYS A 755 CYS A 763 1555 1555 2.03 SSBOND 7 CYS B 665 CYS B 696 1555 1555 2.03 SSBOND 8 CYS B 669 CYS B 701 1555 1555 2.03 SSBOND 9 CYS B 680 CYS B 686 1555 1555 2.03 SSBOND 10 CYS B 755 CYS B 763 1555 1555 2.02 LINK CD1 TRP A 656 C1 MAN A 801 1555 1555 1.49 LINK CD1 TRP A 659 C1 MAN A 811 1555 1555 1.49 LINK CD1 TRP B 656 C1 MAN B 810 1555 1555 1.49 LINK CD1 TRP B 659 C1 MAN B 809 1555 1555 1.49 CISPEP 1 GLY A 683 PRO A 684 0 -0.51 CISPEP 2 GLY B 683 PRO B 684 0 12.45 CRYST1 51.894 68.347 85.502 90.00 90.00 90.00 P 21 21 21 8 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 0.019270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011696 0.00000