HEADER SIGNALING PROTEIN 15-FEB-23 8CKM TITLE SEMAPHORIN-5A TSR 3-4 DOMAINS 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 1 28-FEB-24 8CKM 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 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19RC5_4047 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 7192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.290 REMARK 3 R VALUE (WORKING SET) : 0.288 REMARK 3 FREE R VALUE : 0.331 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 334 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 51.4000 - 3.4300 1.00 3529 177 0.2609 0.3095 REMARK 3 2 3.4300 - 2.7200 0.96 3329 157 0.4324 0.4491 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) : 0.514 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 46.727 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 146.2 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 : 0.003 1615 REMARK 3 ANGLE : 0.506 2203 REMARK 3 CHIRALITY : 0.036 227 REMARK 3 PLANARITY : 0.004 290 REMARK 3 DIHEDRAL : 10.938 573 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 656:663 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.615 -23.615 51.257 REMARK 3 T TENSOR REMARK 3 T11: 2.1041 T22: 2.5645 REMARK 3 T33: 1.5847 T12: 0.5616 REMARK 3 T13: 0.3784 T23: -0.4600 REMARK 3 L TENSOR REMARK 3 L11: 2.1702 L22: 1.4011 REMARK 3 L33: 1.3527 L12: 1.6816 REMARK 3 L13: 0.5779 L23: 0.5758 REMARK 3 S TENSOR REMARK 3 S11: -1.7876 S12: 1.0074 S13: 0.6727 REMARK 3 S21: -1.4399 S22: 4.5810 S23: 3.3327 REMARK 3 S31: -3.1312 S32: -0.0243 S33: -1.1798 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 664:702 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.360 -20.951 57.408 REMARK 3 T TENSOR REMARK 3 T11: 1.7667 T22: 1.8640 REMARK 3 T33: 1.1016 T12: 0.4506 REMARK 3 T13: -0.1428 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 5.0009 L22: 4.2999 REMARK 3 L33: 8.5417 L12: -0.4732 REMARK 3 L13: 0.6166 L23: 4.6656 REMARK 3 S TENSOR REMARK 3 S11: -0.6449 S12: -1.3019 S13: -0.0576 REMARK 3 S21: -0.3182 S22: 1.1585 S23: 0.1405 REMARK 3 S31: 0.8811 S32: 0.1276 S33: -1.1827 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 703:729 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.461 10.759 93.998 REMARK 3 T TENSOR REMARK 3 T11: 0.7788 T22: 1.1670 REMARK 3 T33: 1.2638 T12: 0.0651 REMARK 3 T13: 0.0586 T23: 0.1260 REMARK 3 L TENSOR REMARK 3 L11: 6.0577 L22: 3.7155 REMARK 3 L33: 4.6031 L12: 0.5070 REMARK 3 L13: 0.3929 L23: 4.1498 REMARK 3 S TENSOR REMARK 3 S11: 0.0240 S12: -0.1857 S13: 0.7754 REMARK 3 S21: -0.0660 S22: -1.0428 S23: 0.2312 REMARK 3 S31: -0.2181 S32: -0.7628 S33: 0.6666 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 730:736 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.596 -0.782 85.680 REMARK 3 T TENSOR REMARK 3 T11: 0.8283 T22: 1.7403 REMARK 3 T33: 1.3362 T12: 0.0024 REMARK 3 T13: 0.0531 T23: 0.4709 REMARK 3 L TENSOR REMARK 3 L11: 9.1497 L22: 3.7892 REMARK 3 L33: 6.6293 L12: -2.9579 REMARK 3 L13: -0.9444 L23: 4.4669 REMARK 3 S TENSOR REMARK 3 S11: -2.3315 S12: 1.2297 S13: -0.2515 REMARK 3 S21: -0.5950 S22: 2.1066 S23: 2.4905 REMARK 3 S31: -1.2955 S32: 4.7801 S33: 0.5686 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 737:755 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.184 6.078 84.223 REMARK 3 T TENSOR REMARK 3 T11: 0.9321 T22: 0.9265 REMARK 3 T33: 0.9137 T12: 0.2571 REMARK 3 T13: 0.0890 T23: 0.2574 REMARK 3 L TENSOR REMARK 3 L11: 6.3888 L22: 4.2395 REMARK 3 L33: 3.9215 L12: -1.4776 REMARK 3 L13: -0.1207 L23: 7.1736 REMARK 3 S TENSOR REMARK 3 S11: 0.3159 S12: 2.4377 S13: 0.5141 REMARK 3 S21: 0.2689 S22: -0.7257 S23: 0.3230 REMARK 3 S31: 0.2677 S32: -2.0651 S33: -0.4272 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN B AND RESID 655:663 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.622 -33.679 54.011 REMARK 3 T TENSOR REMARK 3 T11: 2.0192 T22: 1.2023 REMARK 3 T33: 1.4994 T12: 0.0436 REMARK 3 T13: 0.3315 T23: -0.1245 REMARK 3 L TENSOR REMARK 3 L11: 1.9184 L22: 3.2339 REMARK 3 L33: 6.4362 L12: 0.4818 REMARK 3 L13: 0.5038 L23: 0.5006 REMARK 3 S TENSOR REMARK 3 S11: -0.5371 S12: -0.8299 S13: -0.8208 REMARK 3 S21: 1.3024 S22: -1.5645 S23: 3.4092 REMARK 3 S31: 1.2254 S32: -1.2863 S33: 2.6911 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN B AND RESID 664:702 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.089 -25.234 58.319 REMARK 3 T TENSOR REMARK 3 T11: 2.1732 T22: 1.3305 REMARK 3 T33: 1.1657 T12: 0.3830 REMARK 3 T13: 0.0576 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 0.4662 L22: 0.4706 REMARK 3 L33: -0.3017 L12: -2.1383 REMARK 3 L13: 0.1924 L23: 0.5630 REMARK 3 S TENSOR REMARK 3 S11: 0.4801 S12: 0.1973 S13: -0.3623 REMARK 3 S21: -0.2816 S22: 0.1902 S23: -1.1718 REMARK 3 S31: 1.0523 S32: 1.1549 S33: -0.0845 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN B AND RESID 703:728 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.157 8.011 93.985 REMARK 3 T TENSOR REMARK 3 T11: 0.6805 T22: 0.9504 REMARK 3 T33: 1.6565 T12: -0.0257 REMARK 3 T13: 0.1063 T23: 0.1933 REMARK 3 L TENSOR REMARK 3 L11: 8.0426 L22: 6.1955 REMARK 3 L33: 5.5387 L12: -1.2954 REMARK 3 L13: -0.8751 L23: -0.2482 REMARK 3 S TENSOR REMARK 3 S11: -0.2717 S12: -0.1573 S13: 1.9493 REMARK 3 S21: 0.4575 S22: -0.2991 S23: 0.1543 REMARK 3 S31: -0.1726 S32: 0.8444 S33: -0.2234 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN B AND RESID 729:752 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.042 -0.150 86.124 REMARK 3 T TENSOR REMARK 3 T11: 0.8985 T22: 1.4563 REMARK 3 T33: 0.9876 T12: 0.0939 REMARK 3 T13: 0.2205 T23: 0.3525 REMARK 3 L TENSOR REMARK 3 L11: 2.6658 L22: 6.0689 REMARK 3 L33: 8.8443 L12: -0.4856 REMARK 3 L13: 0.6405 L23: 4.0519 REMARK 3 S TENSOR REMARK 3 S11: 0.0426 S12: 0.5734 S13: 0.4573 REMARK 3 S21: -0.0102 S22: -0.1906 S23: 0.1464 REMARK 3 S31: 0.7966 S32: 0.1613 S33: 0.3543 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN B AND RESID 753:764 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.455 23.202 104.492 REMARK 3 T TENSOR REMARK 3 T11: 2.1836 T22: 1.3500 REMARK 3 T33: 3.4254 T12: -0.3247 REMARK 3 T13: -0.5081 T23: -0.5356 REMARK 3 L TENSOR REMARK 3 L11: 0.5908 L22: 3.5841 REMARK 3 L33: 1.9154 L12: 0.8252 REMARK 3 L13: 1.8098 L23: -1.2268 REMARK 3 S TENSOR REMARK 3 S11: -0.9417 S12: -1.4201 S13: 3.4641 REMARK 3 S21: 2.1451 S22: -3.3063 S23: 2.6355 REMARK 3 S31: -5.7752 S32: 0.6332 S33: -0.3845 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN B AND RESID 765:772 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.878 36.878 100.765 REMARK 3 T TENSOR REMARK 3 T11: 1.0384 T22: 1.6065 REMARK 3 T33: 1.1863 T12: 0.0730 REMARK 3 T13: -0.0370 T23: -0.0584 REMARK 3 L TENSOR REMARK 3 L11: 4.4510 L22: 3.1644 REMARK 3 L33: 4.8226 L12: -1.8620 REMARK 3 L13: -4.3386 L23: 0.4758 REMARK 3 S TENSOR REMARK 3 S11: -0.2533 S12: -0.8180 S13: -0.5939 REMARK 3 S21: -1.3820 S22: 1.0577 S23: -1.2126 REMARK 3 S31: 0.5509 S32: 1.1793 S33: -0.2156 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 8CKM 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_1292128652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.9999 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20200417 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7316 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 51.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 5.12900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.300 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 (%): 47.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 38 % PEG 200, 0.1 M SODIUM CITRATE, PH REMARK 280 5.5, 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 52.05500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.82500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.05500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.82500 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 GLY A 651 REMARK 465 PRO A 652 REMARK 465 HIS A 653 REMARK 465 MET A 654 REMARK 465 PHE A 655 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 756 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 MET B 654 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 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 ARG A 664 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 LYS A 705 CG CD CE NZ REMARK 470 ARG A 747 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 754 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 663 CG CD OE1 OE2 REMARK 470 ARG B 664 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 668 CG CD OE1 NE2 REMARK 470 ASN B 682 CG OD1 ND2 REMARK 470 ASP B 685 CG OD1 OD2 REMARK 470 LYS B 705 CG CD CE NZ REMARK 470 HIS B 724 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 744 CG CD OE1 OE2 REMARK 470 ARG B 747 CG CD NE CZ NH1 NH2 REMARK 470 SER B 764 OG 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 -153.43 -82.92 REMARK 500 GLU B 663 -133.94 59.12 REMARK 500 ALA B 687 36.37 -85.48 REMARK 500 SER B 756 -162.52 65.75 REMARK 500 THR B 760 -86.02 -134.01 REMARK 500 SER B 761 -108.48 51.73 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: 8CKL RELATED DB: PDB REMARK 900 8CKL CONTAINS THE SAME PROTEIN COMPLEXED WITH SUCROSE OCTASULFATE DBREF 8CKM A 652 768 UNP Q13591 SEM5A_HUMAN 652 768 DBREF 8CKM B 652 768 UNP Q13591 SEM5A_HUMAN 652 768 SEQADV 8CKM GLU A 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKM THR A 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKM GLY A 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKM GLY A 766 UNP Q13591 ASP 766 CONFLICT SEQADV 8CKM THR A 767 UNP Q13591 GLY 767 CONFLICT SEQADV 8CKM GLU A 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKM VAL A 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKM LEU A 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKM PHE A 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKM GLN A 773 UNP Q13591 EXPRESSION TAG SEQADV 8CKM GLU B 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKM THR B 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKM GLY B 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKM GLY B 766 UNP Q13591 ASP 766 CONFLICT SEQADV 8CKM THR B 767 UNP Q13591 GLY 767 CONFLICT SEQADV 8CKM GLU B 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKM VAL B 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKM LEU B 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKM PHE B 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKM 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 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 CYS A 733 N LYS A 706 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 749 N ARG A 730 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 GLY B 672 ARG B 677 0 SHEET 2 AA6 2 VAL B 691 CYS B 696 -1 O GLU B 692 N ARG B 676 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 2.03 SSBOND 5 CYS A 733 CYS B 733 1555 1555 2.03 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 SSBOND 9 CYS B 755 CYS B 763 1555 1555 2.03 CRYST1 104.110 27.650 92.240 90.00 99.10 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 0.009605 0.000000 0.001539 0.00000 SCALE2 0.000000 0.036166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010979 0.00000