HEADER SIGNALING PROTEIN 15-FEB-23 8CKL TITLE SEMAPHORIN-5A TSR 3-4 DOMAINS IN COMPLEX WITH SUCROSE OCTASULFATE TITLE 2 (SOS) 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_PLASMID: 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 2 11-SEP-24 8CKL 1 JRNL REVDAT 1 28-FEB-24 8CKL 0 JRNL AUTH G.N.NAGY,X.F.ZHAO,R.KARLSSON,K.WANG,R.DUMAN,K.HARLOS, JRNL AUTH 2 K.EL OMARI,A.WAGNER,H.CLAUSEN,R.L.MILLER,R.J.GIGER,E.Y.JONES JRNL TITL STRUCTURE AND FUNCTION OF SEMAPHORIN-5A GLYCOSAMINOGLYCAN JRNL TITL 2 INTERACTIONS. JRNL REF NAT COMMUN V. 15 2723 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38548715 JRNL DOI 10.1038/S41467-024-46725-7 REMARK 2 REMARK 2 RESOLUTION. 2.56 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 55.8 REMARK 3 NUMBER OF REFLECTIONS : 4996 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 239 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 82.9000 - 3.2300 0.85 3691 181 0.2464 0.2663 REMARK 3 2 3.2300 - 2.5600 0.26 1066 58 0.3658 0.4658 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) : 0.409 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.055 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 82.26 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 1659 REMARK 3 ANGLE : 0.562 2276 REMARK 3 CHIRALITY : 0.039 243 REMARK 3 PLANARITY : 0.005 276 REMARK 3 DIHEDRAL : 11.360 595 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 654 THROUGH 696 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2682 -18.0142 5.6666 REMARK 3 T TENSOR REMARK 3 T11: 1.8258 T22: 0.4479 REMARK 3 T33: 0.7260 T12: 0.0093 REMARK 3 T13: 0.0854 T23: -0.1029 REMARK 3 L TENSOR REMARK 3 L11: 1.7192 L22: 2.8335 REMARK 3 L33: 2.9453 L12: 1.4731 REMARK 3 L13: 2.0552 L23: 1.8392 REMARK 3 S TENSOR REMARK 3 S11: 0.1383 S12: 0.3905 S13: -0.2934 REMARK 3 S21: -0.6127 S22: 0.8508 S23: -0.8568 REMARK 3 S31: 0.1171 S32: 0.3212 S33: -0.4360 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 697 THROUGH 756 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8737 13.2720 39.0086 REMARK 3 T TENSOR REMARK 3 T11: -0.0729 T22: 0.3248 REMARK 3 T33: 0.5315 T12: -0.0229 REMARK 3 T13: 0.1126 T23: 0.1352 REMARK 3 L TENSOR REMARK 3 L11: 2.2132 L22: 1.8412 REMARK 3 L33: 2.5554 L12: -0.4040 REMARK 3 L13: 0.0752 L23: -0.4000 REMARK 3 S TENSOR REMARK 3 S11: 0.0520 S12: -0.0486 S13: 0.1917 REMARK 3 S21: -0.3485 S22: 0.2418 S23: 0.5560 REMARK 3 S31: 0.1191 S32: -0.4636 S33: 1.2660 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 654 THROUGH 677 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8880 -21.6606 12.1328 REMARK 3 T TENSOR REMARK 3 T11: 1.4137 T22: 0.1411 REMARK 3 T33: 0.2024 T12: 0.0816 REMARK 3 T13: -0.1231 T23: -0.0306 REMARK 3 L TENSOR REMARK 3 L11: 0.9800 L22: 0.9732 REMARK 3 L33: 1.2926 L12: 0.5402 REMARK 3 L13: -0.2847 L23: 0.7437 REMARK 3 S TENSOR REMARK 3 S11: -0.3164 S12: 0.1860 S13: -0.4178 REMARK 3 S21: -0.5716 S22: 0.1178 S23: 0.0228 REMARK 3 S31: 1.1388 S32: 0.0380 S33: -1.0394 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 678 THROUGH 690 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2299 -34.0112 4.6764 REMARK 3 T TENSOR REMARK 3 T11: 1.9984 T22: 0.5692 REMARK 3 T33: 0.9994 T12: 0.2792 REMARK 3 T13: 0.0798 T23: 0.2783 REMARK 3 L TENSOR REMARK 3 L11: 2.4174 L22: 7.0192 REMARK 3 L33: 1.5139 L12: 1.0708 REMARK 3 L13: -1.9052 L23: -1.0969 REMARK 3 S TENSOR REMARK 3 S11: 0.2963 S12: 0.1456 S13: -0.9283 REMARK 3 S21: -1.9133 S22: -0.1126 S23: 0.2262 REMARK 3 S31: 0.6202 S32: 0.1897 S33: 0.2520 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 691 THROUGH 696 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7773 -17.7811 9.8799 REMARK 3 T TENSOR REMARK 3 T11: 1.9233 T22: 0.4807 REMARK 3 T33: 1.0899 T12: -0.1611 REMARK 3 T13: -0.3716 T23: 0.1216 REMARK 3 L TENSOR REMARK 3 L11: 4.8935 L22: 4.9532 REMARK 3 L33: 0.4951 L12: -0.6939 REMARK 3 L13: -0.4579 L23: -1.2674 REMARK 3 S TENSOR REMARK 3 S11: -0.6839 S12: 0.2070 S13: -1.0586 REMARK 3 S21: -1.4401 S22: -0.0382 S23: 0.1306 REMARK 3 S31: 0.3356 S32: -0.0559 S33: 0.5548 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 697 THROUGH 712 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.4789 4.4574 31.4319 REMARK 3 T TENSOR REMARK 3 T11: 0.0008 T22: 0.5238 REMARK 3 T33: 0.5361 T12: 0.0763 REMARK 3 T13: -0.0111 T23: 0.1155 REMARK 3 L TENSOR REMARK 3 L11: 1.8505 L22: 4.3718 REMARK 3 L33: 2.2699 L12: -1.2715 REMARK 3 L13: -1.4561 L23: -0.9928 REMARK 3 S TENSOR REMARK 3 S11: -0.0259 S12: 0.2933 S13: -0.0936 REMARK 3 S21: -0.8465 S22: -0.3495 S23: 0.1747 REMARK 3 S31: 0.6139 S32: -0.4410 S33: -0.1009 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 713 THROUGH 729 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3325 22.1807 49.5218 REMARK 3 T TENSOR REMARK 3 T11: 0.1882 T22: 0.5066 REMARK 3 T33: 0.7892 T12: 0.0701 REMARK 3 T13: 0.0373 T23: 0.1727 REMARK 3 L TENSOR REMARK 3 L11: 4.7531 L22: 3.8117 REMARK 3 L33: 5.7368 L12: -3.1093 REMARK 3 L13: -2.4081 L23: -1.2524 REMARK 3 S TENSOR REMARK 3 S11: 0.0214 S12: -0.1753 S13: 1.1729 REMARK 3 S21: 0.4662 S22: 0.8919 S23: 0.3016 REMARK 3 S31: -0.3951 S32: 0.1724 S33: 0.0994 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 730 THROUGH 742 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.5236 4.1256 32.4803 REMARK 3 T TENSOR REMARK 3 T11: 0.3998 T22: 0.2791 REMARK 3 T33: 0.7721 T12: -0.0196 REMARK 3 T13: 0.0742 T23: -0.0332 REMARK 3 L TENSOR REMARK 3 L11: 0.4731 L22: 4.3218 REMARK 3 L33: 5.7638 L12: 1.1005 REMARK 3 L13: 1.4865 L23: 2.0474 REMARK 3 S TENSOR REMARK 3 S11: -0.1283 S12: 0.1933 S13: -1.1767 REMARK 3 S21: -0.1578 S22: 0.1773 S23: -0.0101 REMARK 3 S31: 1.4557 S32: -0.0272 S33: 0.0309 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 743 THROUGH 752 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0508 11.3366 44.4747 REMARK 3 T TENSOR REMARK 3 T11: 0.0905 T22: 0.5117 REMARK 3 T33: 0.3220 T12: -0.0634 REMARK 3 T13: 0.0243 T23: -0.1399 REMARK 3 L TENSOR REMARK 3 L11: 3.6048 L22: 2.5707 REMARK 3 L33: 3.0851 L12: 1.7122 REMARK 3 L13: 3.1225 L23: 0.6742 REMARK 3 S TENSOR REMARK 3 S11: 0.1810 S12: -0.0651 S13: -0.5428 REMARK 3 S21: 0.1085 S22: 0.1512 S23: 0.1591 REMARK 3 S31: 0.2997 S32: -0.3368 S33: 0.4247 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 753 THROUGH 773 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0858 45.2014 51.6573 REMARK 3 T TENSOR REMARK 3 T11: 0.1351 T22: 0.6002 REMARK 3 T33: 0.6226 T12: 0.1343 REMARK 3 T13: 0.0426 T23: -0.1854 REMARK 3 L TENSOR REMARK 3 L11: 1.5371 L22: 0.1637 REMARK 3 L33: 0.8948 L12: -0.3303 REMARK 3 L13: -0.0596 L23: -0.2215 REMARK 3 S TENSOR REMARK 3 S11: 0.3001 S12: 0.1882 S13: 0.0383 REMARK 3 S21: -0.0696 S22: 0.0412 S23: -0.0282 REMARK 3 S31: -0.0278 S32: 0.1246 S33: 1.1023 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and ((resid 654 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 655 through 684 or (resid 685 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 686 through 702 REMARK 3 or (resid 703 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 704 through 735 or (resid 736 and (name N REMARK 3 or name CA or name C or name O or name CB REMARK 3 )) or resid 737 through 753 or (resid 754 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 755)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 654 through 675 or REMARK 3 (resid 676 through 677 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 678 or (resid 679 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 680 or (resid 681 through 682 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 683 through 746 REMARK 3 or (resid 747 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 748 through 755)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8CKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-20 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 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 BUILT 20200417 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5008 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 82.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 55.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 10.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 2.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 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 (%): 48.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8 % PEG 8000, 0.1 M SODIUM CITRATE, PH REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 53.05300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.05300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.38500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, H 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 GLY A 651 REMARK 465 PRO A 652 REMARK 465 HIS A 653 REMARK 465 ASN A 717 REMARK 465 ILE A 718 REMARK 465 SER A 719 REMARK 465 ASP A 720 REMARK 465 ASN A 721 REMARK 465 GLY A 722 REMARK 465 GLY A 723 REMARK 465 SER A 757 REMARK 465 ASP A 758 REMARK 465 GLY A 759 REMARK 465 THR A 760 REMARK 465 SER A 761 REMARK 465 GLY A 762 REMARK 465 CYS A 763 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 PRO B 652 REMARK 465 HIS B 653 REMARK 465 ASN B 717 REMARK 465 ILE B 718 REMARK 465 SER B 719 REMARK 465 ASP B 720 REMARK 465 ASN B 721 REMARK 465 GLY B 722 REMARK 465 GLY B 723 REMARK 465 SER B 756 REMARK 465 SER B 757 REMARK 465 ASP B 758 REMARK 465 GLY B 759 REMARK 465 THR B 760 REMARK 465 SER B 761 REMARK 465 GLY B 762 REMARK 465 CYS B 763 REMARK 465 SER B 764 REMARK 465 THR B 765 REMARK 465 GLY B 766 REMARK 465 THR B 767 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 ARG A 664 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 668 CG CD OE1 NE2 REMARK 470 ARG A 676 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 677 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 679 CG1 CG2 CD1 REMARK 470 GLU A 681 CG CD OE1 OE2 REMARK 470 ASN A 682 CG OD1 ND2 REMARK 470 GLU A 744 CG CD OE1 OE2 REMARK 470 ARG A 747 CG CD NE CZ NH1 NH2 REMARK 470 MET B 654 CG SD CE REMARK 470 ARG B 664 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 668 CG CD OE1 NE2 REMARK 470 ARG B 677 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 685 CG OD1 OD2 REMARK 470 GLU B 703 CG CD OE1 OE2 REMARK 470 ARG B 736 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 744 CG CD OE1 OE2 REMARK 470 TYR B 754 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 769 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE ARG A 749 OE2 GLU A 751 2556 2.19 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 GLU A 663 -169.29 -77.72 REMARK 500 GLU B 663 -168.49 64.60 REMARK 500 PHE B 772 41.20 -97.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8CKG RELATED DB: PDB REMARK 900 8CKG CONTAINS THE SAME PROTEIN COMPLEXED WITH SULFATE REMARK 900 RELATED ID: 8CKK RELATED DB: PDB REMARK 900 8CKK CONTAINS THE SAME PROTEIN COMPLEXED WITH NITRATE REMARK 900 RELATED ID: 8CKM RELATED DB: PDB REMARK 900 8CKM CONTAINS THE SAME PROTEIN IN APO STATE DBREF 8CKL A 652 765 UNP Q13591 SEM5A_HUMAN 652 765 DBREF 8CKL B 652 765 UNP Q13591 SEM5A_HUMAN 652 765 SEQADV 8CKL GLU A 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKL THR A 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLY A 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLY A 766 UNP Q13591 EXPRESSION TAG SEQADV 8CKL THR A 767 UNP Q13591 EXPRESSION TAG SEQADV 8CKL LEU A 768 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLU A 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKL VAL A 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKL LEU A 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKL PHE A 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLN A 773 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLU B 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKL THR B 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLY B 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLY B 766 UNP Q13591 EXPRESSION TAG SEQADV 8CKL THR B 767 UNP Q13591 EXPRESSION TAG SEQADV 8CKL LEU B 768 UNP Q13591 EXPRESSION TAG SEQADV 8CKL GLU B 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKL VAL B 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKL LEU B 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKL PHE B 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKL 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 YYJ H 2 28 HET GU4 H 1 27 HET MAN A 801 11 HET MAN A 802 11 HET MAN B 801 11 HET MAN B 802 11 HETNAM YYJ 1,3,4,6-TETRA-O-SULFO-BETA-D-FRUCTOFURANOSE HETNAM GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOSE; 2,3,4,6- HETSYN 2 GU4 TETRA-O-SULFONATO-D-GLUCOSE; 2,3,4,6-TETRA-O- HETSYN 3 GU4 SULFONATO-GLUCOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 YYJ C6 H12 O18 S4 FORMUL 3 GU4 C6 H12 O18 S4 FORMUL 4 MAN 4(C6 H12 O6) HELIX 1 AA1 ASP A 739 ASN A 741 5 3 HELIX 2 AA2 ASP B 739 ASN B 741 5 3 SHEET 1 AA1 2 GLY A 672 ARG A 677 0 SHEET 2 AA1 2 VAL A 691 CYS A 696 -1 O GLN A 694 N GLN A 674 SHEET 1 AA2 3 GLU A 703 THR A 707 0 SHEET 2 AA2 3 THR A 732 ARG A 736 -1 O ALA A 735 N LEU A 704 SHEET 3 AA2 3 LEU B 743 VAL B 745 -1 O GLU B 744 N LYS A 734 SHEET 1 AA3 3 THR A 714 PRO A 715 0 SHEET 2 AA3 3 TYR A 725 ARG A 730 -1 O GLN A 727 N THR A 714 SHEET 3 AA3 3 ARG B 749 TYR B 754 -1 O ARG B 753 N GLU A 726 SHEET 1 AA4 3 LEU A 743 VAL A 745 0 SHEET 2 AA4 3 THR B 732 ARG B 736 -1 O LYS B 734 N GLU A 744 SHEET 3 AA4 3 GLU B 703 THR B 707 -1 N LYS B 706 O CYS B 733 SHEET 1 AA5 3 ARG A 749 TYR A 754 0 SHEET 2 AA5 3 TYR B 725 ARG B 730 -1 O GLU B 726 N ARG A 753 SHEET 3 AA5 3 THR B 714 PRO B 715 -1 N THR B 714 O GLN B 727 SHEET 1 AA6 2 PHE B 655 TRP B 656 0 SHEET 2 AA6 2 CYS B 680 GLU B 681 -1 O GLU B 681 N PHE B 655 SHEET 1 AA7 2 GLY B 672 ARG B 677 0 SHEET 2 AA7 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 2.03 SSBOND 3 CYS A 680 CYS A 686 1555 1555 2.03 SSBOND 4 CYS A 689 CYS B 689 1555 1555 2.00 SSBOND 5 CYS A 733 CYS B 733 1555 1555 2.00 SSBOND 6 CYS B 665 CYS B 696 1555 1555 2.03 SSBOND 7 CYS B 669 CYS B 701 1555 1555 2.03 SSBOND 8 CYS B 680 CYS B 686 1555 1555 2.03 LINK CD1 TRP A 656 C1 MAN A 802 1555 1555 1.49 LINK CD1 TRP A 659 C1 MAN A 801 1555 1555 1.49 LINK CD1 TRP B 656 C1 MAN B 801 1555 1555 1.49 LINK CD1 TRP B 659 C1 MAN B 802 1555 1555 1.49 LINK C1 GU4 H 1 O2 YYJ H 2 1555 1555 1.45 CRYST1 106.106 30.770 84.172 90.00 99.97 90.00 C 1 2 1 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 0.009425 0.000000 0.001657 0.00000 SCALE2 0.000000 0.032499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012063 0.00000 MTRIX1 1 -0.966373 -0.205421 -0.154678 19.38841 1 MTRIX2 1 -0.165335 0.035661 0.985593 -26.30252 1 MTRIX3 1 -0.196945 0.978024 -0.068425 30.76039 1