HEADER SIGNALING PROTEIN 15-FEB-23 8CKG TITLE SEMAPHORIN-5A TSR 3-4 DOMAINS IN COMPLEX WITH SULFATE 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 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 8CKG 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 SULFATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.71 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 70.6 REMARK 3 NUMBER OF REFLECTIONS : 20984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 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 51.6700 - 3.2800 1.00 4187 204 0.1835 0.1861 REMARK 3 2 3.2800 - 2.6000 1.00 4056 214 0.2180 0.2900 REMARK 3 3 2.6000 - 2.2700 0.99 3980 196 0.2345 0.2674 REMARK 3 4 2.2700 - 2.0700 0.84 3397 163 0.2229 0.2420 REMARK 3 5 2.0700 - 1.9200 0.64 2560 121 0.2351 0.2781 REMARK 3 6 1.9100 - 1.8000 0.40 1422 93 0.2853 0.2671 REMARK 3 7 1.8000 - 1.7140 0.09 375 9 0.3149 0.3772 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1741 REMARK 3 ANGLE : 0.872 2365 REMARK 3 CHIRALITY : 0.050 247 REMARK 3 PLANARITY : 0.006 301 REMARK 3 DIHEDRAL : 12.701 646 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 654 THROUGH 696 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7229 -23.5574 51.1902 REMARK 3 T TENSOR REMARK 3 T11: 1.6447 T22: 0.6444 REMARK 3 T33: 0.1482 T12: 0.3392 REMARK 3 T13: -0.1122 T23: -0.0725 REMARK 3 L TENSOR REMARK 3 L11: 1.2723 L22: 1.1418 REMARK 3 L33: 4.4204 L12: 0.1646 REMARK 3 L13: 0.0556 L23: 1.8334 REMARK 3 S TENSOR REMARK 3 S11: 0.2531 S12: 0.7113 S13: -0.1639 REMARK 3 S21: -1.3790 S22: 0.1066 S23: -0.1288 REMARK 3 S31: 0.3245 S32: 0.2786 S33: 0.3709 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 697 THROUGH 707 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6787 -6.7000 75.7410 REMARK 3 T TENSOR REMARK 3 T11: 0.2086 T22: 0.2613 REMARK 3 T33: 0.2665 T12: 0.0530 REMARK 3 T13: -0.0152 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.9536 L22: 9.5258 REMARK 3 L33: 4.9612 L12: -3.4212 REMARK 3 L13: -2.2494 L23: 4.8863 REMARK 3 S TENSOR REMARK 3 S11: 0.0247 S12: -0.1325 S13: 0.2609 REMARK 3 S21: 0.1255 S22: 0.2680 S23: -0.4806 REMARK 3 S31: 0.4580 S32: 0.3911 S33: -0.2389 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 708 THROUGH 729 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5356 14.6438 94.7009 REMARK 3 T TENSOR REMARK 3 T11: 0.1601 T22: 0.2019 REMARK 3 T33: 0.3305 T12: -0.0117 REMARK 3 T13: 0.0222 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 3.4683 L22: 5.6630 REMARK 3 L33: 9.5011 L12: 3.4020 REMARK 3 L13: 5.4286 L23: 4.9104 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: -0.3870 S13: 0.4746 REMARK 3 S21: 0.2267 S22: -0.2005 S23: 0.3806 REMARK 3 S31: -0.1475 S32: -0.4049 S33: 0.0125 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 730 THROUGH 742 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5329 -0.6512 78.2639 REMARK 3 T TENSOR REMARK 3 T11: 0.1650 T22: 0.2412 REMARK 3 T33: 0.2493 T12: 0.0594 REMARK 3 T13: -0.0343 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 5.1628 L22: 5.6474 REMARK 3 L33: 4.2089 L12: -2.2773 REMARK 3 L13: -3.7954 L23: 3.1946 REMARK 3 S TENSOR REMARK 3 S11: 0.1853 S12: 0.1766 S13: 0.2373 REMARK 3 S21: -0.0773 S22: 0.0432 S23: -0.0269 REMARK 3 S31: 0.3311 S32: 0.1357 S33: -0.0007 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 743 THROUGH 763 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.0465 10.1140 88.4611 REMARK 3 T TENSOR REMARK 3 T11: 0.0873 T22: 0.2819 REMARK 3 T33: 0.2620 T12: -0.0136 REMARK 3 T13: -0.0353 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 3.7188 L22: 4.0792 REMARK 3 L33: 2.1901 L12: -2.7350 REMARK 3 L13: -2.4809 L23: 0.8843 REMARK 3 S TENSOR REMARK 3 S11: 0.1438 S12: -0.4962 S13: 0.4285 REMARK 3 S21: 0.1098 S22: 0.1438 S23: -0.0158 REMARK 3 S31: -0.2108 S32: 0.3994 S33: -0.3578 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 654 THROUGH 712 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9391 -23.4074 60.9539 REMARK 3 T TENSOR REMARK 3 T11: 1.0046 T22: 0.5903 REMARK 3 T33: 0.4165 T12: 0.0795 REMARK 3 T13: -0.1764 T23: -0.0497 REMARK 3 L TENSOR REMARK 3 L11: 0.2283 L22: 4.0136 REMARK 3 L33: 1.2408 L12: -0.7634 REMARK 3 L13: 0.0332 L23: 1.6161 REMARK 3 S TENSOR REMARK 3 S11: 0.4001 S12: 0.3594 S13: -0.1844 REMARK 3 S21: -1.3615 S22: -0.5575 S23: 0.6760 REMARK 3 S31: 0.6230 S32: -0.2951 S33: 0.1231 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 713 THROUGH 742 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7925 5.1331 87.1861 REMARK 3 T TENSOR REMARK 3 T11: 0.0995 T22: 0.2370 REMARK 3 T33: 0.3063 T12: -0.0431 REMARK 3 T13: -0.0334 T23: 0.0361 REMARK 3 L TENSOR REMARK 3 L11: 3.6310 L22: 5.9721 REMARK 3 L33: 6.6612 L12: -2.1938 REMARK 3 L13: -2.2848 L23: 4.6794 REMARK 3 S TENSOR REMARK 3 S11: 0.2182 S12: -0.0378 S13: 0.2766 REMARK 3 S21: -0.0687 S22: -0.0585 S23: 0.0176 REMARK 3 S31: -0.0056 S32: -0.2347 S33: -0.2068 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 743 THROUGH 772 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1825 20.4218 96.7380 REMARK 3 T TENSOR REMARK 3 T11: 0.2350 T22: 0.2526 REMARK 3 T33: 0.2625 T12: -0.0155 REMARK 3 T13: 0.0097 T23: -0.0259 REMARK 3 L TENSOR REMARK 3 L11: 0.5889 L22: 3.7500 REMARK 3 L33: 0.4482 L12: 1.5695 REMARK 3 L13: 0.6104 L23: 1.4444 REMARK 3 S TENSOR REMARK 3 S11: 0.0619 S12: -0.0142 S13: 0.0832 REMARK 3 S21: 0.1103 S22: -0.0620 S23: 0.1163 REMARK 3 S31: 0.0703 S32: 0.0575 S33: -0.0339 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 8CKG 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_1292128352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-20; 02-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100; 50 REMARK 200 PH : 8.5; 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : DIAMOND; DIAMOND REMARK 200 BEAMLINE : I24; I23 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686; 2.7552 REMARK 200 MONOCHROMATOR : M; M REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M; DECTRIS REMARK 200 PILATUS 12M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20200417 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20985 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.714 REMARK 200 RESOLUTION RANGE LOW (A) : 88.925 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 70.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 16.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2 M LITHIUM SULFATE, REMARK 280 0.1 M TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K. 30% PEG 4000, 0.2 M LITHIUM SULFATE, 0.1 M TRIS, PH 8.5, REMARK 280 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 52.54050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.64300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.54050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.64300 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 942 LIES ON A SPECIAL POSITION. 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 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 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 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 HIS A 724 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 664 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 668 CG CD OE1 NE2 REMARK 470 HIS B 724 CG ND1 CD2 CE1 NE2 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 50.79 -100.32 REMARK 500 GLU B 663 -178.62 59.99 REMARK 500 SER B 756 174.48 72.23 REMARK 500 CYS B 763 -96.14 -113.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES 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 REMARK 900 RELATED ID: 8CKL RELATED DB: PDB REMARK 900 8CKL CONTAINS THE SAME PROTEIN COMPLEXED WITH SUCROSE OCTASULFATE DBREF 8CKG A 652 768 UNP Q13591 SEM5A_HUMAN 652 768 DBREF 8CKG B 652 768 UNP Q13591 SEM5A_HUMAN 652 768 SEQADV 8CKG GLU A 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKG THR A 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKG GLY A 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKG GLY A 766 UNP Q13591 ASP 766 ENGINEERED MUTATION SEQADV 8CKG THR A 767 UNP Q13591 GLY 767 ENGINEERED MUTATION SEQADV 8CKG GLU A 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKG VAL A 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKG LEU A 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKG PHE A 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKG GLN A 773 UNP Q13591 EXPRESSION TAG SEQADV 8CKG GLU B 649 UNP Q13591 EXPRESSION TAG SEQADV 8CKG THR B 650 UNP Q13591 EXPRESSION TAG SEQADV 8CKG GLY B 651 UNP Q13591 EXPRESSION TAG SEQADV 8CKG GLY B 766 UNP Q13591 ASP 766 ENGINEERED MUTATION SEQADV 8CKG THR B 767 UNP Q13591 GLY 767 ENGINEERED MUTATION SEQADV 8CKG GLU B 769 UNP Q13591 EXPRESSION TAG SEQADV 8CKG VAL B 770 UNP Q13591 EXPRESSION TAG SEQADV 8CKG LEU B 771 UNP Q13591 EXPRESSION TAG SEQADV 8CKG PHE B 772 UNP Q13591 EXPRESSION TAG SEQADV 8CKG 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 SO4 A 801 5 HET MAN A 802 11 HET MAN A 803 11 HET SO4 B 801 5 HET MAN B 802 11 HET MAN B 803 11 HETNAM SO4 SULFATE ION HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 MAN 4(C6 H12 O6) FORMUL 9 HOH *99(H2 O) 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 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 TYR A 725 ARG A 730 -1 O GLN A 727 N THR A 714 SHEET 3 AA4 3 ARG B 749 TYR B 754 -1 O ARG B 749 N ARG A 730 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 TYR A 754 0 SHEET 2 AA6 3 TYR B 725 ARG B 730 -1 O GLU B 726 N ARG A 753 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 GLU B 692 N ARG B 676 SSBOND 1 CYS A 665 CYS A 696 1555 1555 2.05 SSBOND 2 CYS A 669 CYS A 701 1555 1555 2.06 SSBOND 3 CYS A 680 CYS A 686 1555 1555 2.04 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 2.05 SSBOND 7 CYS B 665 CYS B 696 1555 1555 2.03 SSBOND 8 CYS B 669 CYS B 701 1555 1555 2.05 SSBOND 9 CYS B 680 CYS B 686 1555 1555 2.05 SSBOND 10 CYS B 755 CYS B 763 1555 1555 2.07 LINK CD1 TRP A 656 C1 MAN A 802 1555 1555 1.49 LINK CD1 TRP A 659 C1 MAN A 803 1555 1555 1.49 LINK CD1 TRP B 656 C1 MAN B 802 1555 1555 1.49 LINK CD1 TRP B 659 C1 MAN B 803 1555 1555 1.49 CRYST1 105.081 29.286 90.429 90.00 100.46 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 0.009516 0.000000 0.001757 0.00000 SCALE2 0.000000 0.034146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011245 0.00000