HEADER SIGNALING PROTEIN 26-FEB-10 3AFC TITLE MOUSE SEMAPHORIN 6A EXTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEMAPHORIN-6A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SEMA AND PSI DOMAIN (UNP RESIDUES 19-570); COMPND 5 SYNONYM: SEMAPHORIN VIA, SEMA VIA, SEMAPHORIN-6A-1, SEMA6A-1, COMPND 6 SEMAPHORIN Q, SEMA Q; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SEMA6A, SEMAQ; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: LEC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSGHV0 KEYWDS BETA PROPELLER, DISULFIDE BOND, GLYCOPROTEIN, NEUROGENESIS, IMMUNE KEYWDS 2 RESPONSE, AXON GUIDANCE, MEMBRANE PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.YASUI,T.NOGI,E.MIHARA,J.TAKAGI REVDAT 6 30-OCT-24 3AFC 1 REMARK REVDAT 5 01-NOV-23 3AFC 1 HETSYN REVDAT 4 29-JUL-20 3AFC 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 03-NOV-10 3AFC 1 JRNL REVDAT 2 27-OCT-10 3AFC 1 JRNL REVDAT 1 06-OCT-10 3AFC 0 JRNL AUTH T.NOGI,N.YASUI,E.MIHARA,Y.MATSUNAGA,M.NODA,N.YAMASHITA, JRNL AUTH 2 T.TOYOFUKU,S.UCHIYAMA,Y.GOSHIMA,A.KUMANOGOH,J.TAKAGI JRNL TITL STRUCTURAL BASIS FOR SEMAPHORIN SIGNALLING THROUGH THE JRNL TITL 2 PLEXIN RECEPTOR. JRNL REF NATURE V. 467 1123 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20881961 JRNL DOI 10.1038/NATURE09473 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 38510 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2083 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8182 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.06000 REMARK 3 B22 (A**2) : -2.08000 REMARK 3 B33 (A**2) : -1.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.727 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.332 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.251 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.102 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8489 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11508 ; 1.180 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1029 ; 6.501 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 387 ;34.933 ;23.411 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1415 ;15.825 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 59 ;19.560 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1266 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6437 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 5152 ; 0.533 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8347 ; 0.998 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3337 ; 1.185 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3159 ; 2.038 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 3AFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000029182. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-09 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40593 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 44.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.38900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 1OLZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-24% (WT/VOL) PEG 1500, 0.1M TRIS-CL REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 44.53000 REMARK 290 SMTRY3 2 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: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLY A 15 REMARK 465 SER A 16 REMARK 465 SER A 17 REMARK 465 ARG A 18 REMARK 465 PRO A 46 REMARK 465 GLY A 47 REMARK 465 ARG A 48 REMARK 465 ASN A 49 REMARK 465 THR A 50 REMARK 465 THR A 51 REMARK 465 GLN A 52 REMARK 465 ARG A 53 REMARK 465 ILE A 454 REMARK 465 GLY A 455 REMARK 465 SER A 456 REMARK 465 SER A 457 REMARK 465 GLY A 458 REMARK 465 PHE A 459 REMARK 465 LEU A 460 REMARK 465 ASN A 461 REMARK 465 HIS A 569 REMARK 465 ASN A 570 REMARK 465 GLY B 15 REMARK 465 SER B 16 REMARK 465 SER B 17 REMARK 465 ARG B 18 REMARK 465 HIS B 44 REMARK 465 LYS B 45 REMARK 465 PRO B 46 REMARK 465 GLY B 47 REMARK 465 ARG B 48 REMARK 465 ASN B 49 REMARK 465 THR B 50 REMARK 465 THR B 51 REMARK 465 GLN B 52 REMARK 465 ARG B 53 REMARK 465 HIS B 54 REMARK 465 THR B 83 REMARK 465 SER B 84 REMARK 465 HIS B 85 REMARK 465 THR B 86 REMARK 465 GLU B 87 REMARK 465 HIS B 518 REMARK 465 GLY B 519 REMARK 465 LYS B 520 REMARK 465 CYS B 521 REMARK 465 LYS B 522 REMARK 465 GLY B 534 REMARK 465 TRP B 535 REMARK 465 VAL B 536 REMARK 465 ARG B 537 REMARK 465 GLU B 538 REMARK 465 SER B 539 REMARK 465 GLY B 540 REMARK 465 SER B 541 REMARK 465 CYS B 542 REMARK 465 ALA B 543 REMARK 465 HIS B 544 REMARK 465 LEU B 545 REMARK 465 SER B 546 REMARK 465 PRO B 547 REMARK 465 LEU B 548 REMARK 465 SER B 549 REMARK 465 ARG B 550 REMARK 465 LEU B 551 REMARK 465 THR B 552 REMARK 465 PHE B 553 REMARK 465 ARG B 559 REMARK 465 GLY B 560 REMARK 465 ASN B 561 REMARK 465 THR B 562 REMARK 465 ASP B 563 REMARK 465 GLY B 564 REMARK 465 LEU B 565 REMARK 465 GLY B 566 REMARK 465 ASP B 567 REMARK 465 CYS B 568 REMARK 465 HIS B 569 REMARK 465 ASN B 570 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 559 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 34 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 516 CG CD OE1 OE2 REMARK 470 ARG B 517 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 523 CG CD CE NZ REMARK 470 GLU B 554 CG CD OE1 OE2 REMARK 470 GLN B 555 CG CD OE1 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 ASN A 65 -105.15 49.57 REMARK 500 ALA A 72 -150.50 -146.83 REMARK 500 ASP A 74 -4.49 60.14 REMARK 500 THR A 83 118.10 -31.20 REMARK 500 THR A 86 -144.59 -97.29 REMARK 500 CYS A 117 66.07 -101.58 REMARK 500 ASN A 128 -157.06 -154.66 REMARK 500 ASN A 141 67.24 -152.44 REMARK 500 THR A 186 -160.29 -171.37 REMARK 500 ALA A 192 41.81 70.49 REMARK 500 LEU A 201 -166.45 72.50 REMARK 500 ASP A 203 17.21 57.25 REMARK 500 THR A 245 -107.09 -69.37 REMARK 500 MET A 246 80.57 -61.31 REMARK 500 MET A 246 79.89 -60.48 REMARK 500 ASN A 320 69.42 -110.82 REMARK 500 SER A 374 -1.85 79.70 REMARK 500 THR A 421 -92.34 -118.68 REMARK 500 GLN A 433 51.21 38.66 REMARK 500 ASP A 480 -115.18 -125.48 REMARK 500 ARG A 514 52.07 -112.39 REMARK 500 SER B 28 124.80 -175.02 REMARK 500 ASN B 65 -113.26 55.60 REMARK 500 ASP B 74 -19.52 70.93 REMARK 500 TRP B 97 86.75 -152.10 REMARK 500 ASN B 128 -171.59 -174.24 REMARK 500 ALA B 163 -1.71 76.22 REMARK 500 THR B 186 -156.90 -175.37 REMARK 500 ASP B 194 78.93 -103.49 REMARK 500 LEU B 201 -175.76 65.17 REMARK 500 SER B 373 120.85 -21.72 REMARK 500 SER B 374 -7.54 64.23 REMARK 500 ILE B 406 -3.73 89.19 REMARK 500 THR B 414 -84.04 -108.94 REMARK 500 ARG B 417 53.99 -96.43 REMARK 500 THR B 421 -97.39 -111.06 REMARK 500 THR B 524 73.16 -104.01 REMARK 500 GLN B 555 91.11 -173.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 3AFC A 19 570 UNP O35464 SEM6A_MOUSE 19 570 DBREF 3AFC B 19 570 UNP O35464 SEM6A_MOUSE 19 570 SEQADV 3AFC GLY A 15 UNP O35464 EXPRESSION TAG SEQADV 3AFC SER A 16 UNP O35464 EXPRESSION TAG SEQADV 3AFC SER A 17 UNP O35464 EXPRESSION TAG SEQADV 3AFC ARG A 18 UNP O35464 EXPRESSION TAG SEQADV 3AFC GLY B 15 UNP O35464 EXPRESSION TAG SEQADV 3AFC SER B 16 UNP O35464 EXPRESSION TAG SEQADV 3AFC SER B 17 UNP O35464 EXPRESSION TAG SEQADV 3AFC ARG B 18 UNP O35464 EXPRESSION TAG SEQRES 1 A 556 GLY SER SER ARG GLY PHE PRO GLU ASP SER GLU PRO ILE SEQRES 2 A 556 SER ILE SER HIS GLY ASN TYR THR LYS GLN TYR PRO VAL SEQRES 3 A 556 PHE VAL GLY HIS LYS PRO GLY ARG ASN THR THR GLN ARG SEQRES 4 A 556 HIS ARG LEU ASP ILE GLN MET ILE MET ILE MET ASN ARG SEQRES 5 A 556 THR LEU TYR VAL ALA ALA ARG ASP HIS ILE TYR THR VAL SEQRES 6 A 556 ASP ILE ASP THR SER HIS THR GLU GLU ILE TYR CYS SER SEQRES 7 A 556 LYS LYS LEU THR TRP LYS SER ARG GLN ALA ASP VAL ASP SEQRES 8 A 556 THR CYS ARG MET LYS GLY LYS HIS LYS ASP GLU CYS HIS SEQRES 9 A 556 ASN PHE ILE LYS VAL LEU LEU LYS LYS ASN ASP ASP THR SEQRES 10 A 556 LEU PHE VAL CYS GLY THR ASN ALA PHE ASN PRO SER CYS SEQRES 11 A 556 ARG ASN TYR ARG VAL ASP THR LEU GLU THR PHE GLY ASP SEQRES 12 A 556 GLU PHE SER GLY MET ALA ARG CYS PRO TYR ASP ALA LYS SEQRES 13 A 556 HIS ALA ASN ILE ALA LEU PHE ALA ASP GLY LYS LEU TYR SEQRES 14 A 556 SER ALA THR VAL THR ASP PHE LEU ALA ILE ASP ALA VAL SEQRES 15 A 556 ILE TYR ARG SER LEU GLY ASP SER PRO THR LEU ARG THR SEQRES 16 A 556 VAL LYS HIS ASP SER LYS TRP LEU LYS GLU PRO TYR PHE SEQRES 17 A 556 VAL GLN ALA VAL ASP TYR GLY ASP TYR ILE TYR PHE PHE SEQRES 18 A 556 PHE ARG GLU ILE ALA VAL GLU TYR ASN THR MET GLY LYS SEQRES 19 A 556 VAL VAL PHE PRO ARG VAL ALA GLN VAL CYS LYS ASN ASP SEQRES 20 A 556 MET GLY GLY SER GLN ARG VAL LEU GLU LYS GLN TRP THR SEQRES 21 A 556 SER PHE LEU LYS ALA ARG LEU ASN CYS SER VAL PRO GLY SEQRES 22 A 556 ASP SER HIS PHE TYR PHE ASN ILE LEU GLN ALA VAL THR SEQRES 23 A 556 ASP VAL ILE ARG ILE ASN GLY ARG ASP VAL VAL LEU ALA SEQRES 24 A 556 THR PHE SER THR PRO TYR ASN SER ILE PRO GLY SER ALA SEQRES 25 A 556 VAL CYS ALA TYR ASP MET LEU ASP ILE ALA ASN VAL PHE SEQRES 26 A 556 THR GLY ARG PHE LYS GLU GLN LYS SER PRO ASP SER THR SEQRES 27 A 556 TRP THR PRO VAL PRO ASP GLU ARG VAL PRO LYS PRO ARG SEQRES 28 A 556 PRO GLY CYS CYS ALA GLY SER SER SER LEU GLU LYS TYR SEQRES 29 A 556 ALA THR SER ASN GLU PHE PRO ASP ASP THR LEU ASN PHE SEQRES 30 A 556 ILE LYS THR HIS PRO LEU MET ASP GLU ALA VAL PRO SER SEQRES 31 A 556 ILE ILE ASN ARG PRO TRP PHE LEU ARG THR MET VAL ARG SEQRES 32 A 556 TYR ARG LEU THR LYS ILE ALA VAL ASP ASN ALA ALA GLY SEQRES 33 A 556 PRO TYR GLN ASN HIS THR VAL VAL PHE LEU GLY SER GLU SEQRES 34 A 556 LYS GLY ILE ILE LEU LYS PHE LEU ALA ARG ILE GLY SER SEQRES 35 A 556 SER GLY PHE LEU ASN GLY SER LEU PHE LEU GLU GLU MET SEQRES 36 A 556 ASN VAL TYR ASN PRO GLU LYS CYS SER TYR ASP GLY VAL SEQRES 37 A 556 GLU ASP LYS ARG ILE MET GLY MET GLN LEU ASP ARG ALA SEQRES 38 A 556 SER GLY SER LEU TYR VAL ALA PHE SER THR CYS VAL ILE SEQRES 39 A 556 LYS VAL PRO LEU GLY ARG CYS GLU ARG HIS GLY LYS CYS SEQRES 40 A 556 LYS LYS THR CYS ILE ALA SER ARG ASP PRO TYR CYS GLY SEQRES 41 A 556 TRP VAL ARG GLU SER GLY SER CYS ALA HIS LEU SER PRO SEQRES 42 A 556 LEU SER ARG LEU THR PHE GLU GLN ASP ILE GLU ARG GLY SEQRES 43 A 556 ASN THR ASP GLY LEU GLY ASP CYS HIS ASN SEQRES 1 B 556 GLY SER SER ARG GLY PHE PRO GLU ASP SER GLU PRO ILE SEQRES 2 B 556 SER ILE SER HIS GLY ASN TYR THR LYS GLN TYR PRO VAL SEQRES 3 B 556 PHE VAL GLY HIS LYS PRO GLY ARG ASN THR THR GLN ARG SEQRES 4 B 556 HIS ARG LEU ASP ILE GLN MET ILE MET ILE MET ASN ARG SEQRES 5 B 556 THR LEU TYR VAL ALA ALA ARG ASP HIS ILE TYR THR VAL SEQRES 6 B 556 ASP ILE ASP THR SER HIS THR GLU GLU ILE TYR CYS SER SEQRES 7 B 556 LYS LYS LEU THR TRP LYS SER ARG GLN ALA ASP VAL ASP SEQRES 8 B 556 THR CYS ARG MET LYS GLY LYS HIS LYS ASP GLU CYS HIS SEQRES 9 B 556 ASN PHE ILE LYS VAL LEU LEU LYS LYS ASN ASP ASP THR SEQRES 10 B 556 LEU PHE VAL CYS GLY THR ASN ALA PHE ASN PRO SER CYS SEQRES 11 B 556 ARG ASN TYR ARG VAL ASP THR LEU GLU THR PHE GLY ASP SEQRES 12 B 556 GLU PHE SER GLY MET ALA ARG CYS PRO TYR ASP ALA LYS SEQRES 13 B 556 HIS ALA ASN ILE ALA LEU PHE ALA ASP GLY LYS LEU TYR SEQRES 14 B 556 SER ALA THR VAL THR ASP PHE LEU ALA ILE ASP ALA VAL SEQRES 15 B 556 ILE TYR ARG SER LEU GLY ASP SER PRO THR LEU ARG THR SEQRES 16 B 556 VAL LYS HIS ASP SER LYS TRP LEU LYS GLU PRO TYR PHE SEQRES 17 B 556 VAL GLN ALA VAL ASP TYR GLY ASP TYR ILE TYR PHE PHE SEQRES 18 B 556 PHE ARG GLU ILE ALA VAL GLU TYR ASN THR MET GLY LYS SEQRES 19 B 556 VAL VAL PHE PRO ARG VAL ALA GLN VAL CYS LYS ASN ASP SEQRES 20 B 556 MET GLY GLY SER GLN ARG VAL LEU GLU LYS GLN TRP THR SEQRES 21 B 556 SER PHE LEU LYS ALA ARG LEU ASN CYS SER VAL PRO GLY SEQRES 22 B 556 ASP SER HIS PHE TYR PHE ASN ILE LEU GLN ALA VAL THR SEQRES 23 B 556 ASP VAL ILE ARG ILE ASN GLY ARG ASP VAL VAL LEU ALA SEQRES 24 B 556 THR PHE SER THR PRO TYR ASN SER ILE PRO GLY SER ALA SEQRES 25 B 556 VAL CYS ALA TYR ASP MET LEU ASP ILE ALA ASN VAL PHE SEQRES 26 B 556 THR GLY ARG PHE LYS GLU GLN LYS SER PRO ASP SER THR SEQRES 27 B 556 TRP THR PRO VAL PRO ASP GLU ARG VAL PRO LYS PRO ARG SEQRES 28 B 556 PRO GLY CYS CYS ALA GLY SER SER SER LEU GLU LYS TYR SEQRES 29 B 556 ALA THR SER ASN GLU PHE PRO ASP ASP THR LEU ASN PHE SEQRES 30 B 556 ILE LYS THR HIS PRO LEU MET ASP GLU ALA VAL PRO SER SEQRES 31 B 556 ILE ILE ASN ARG PRO TRP PHE LEU ARG THR MET VAL ARG SEQRES 32 B 556 TYR ARG LEU THR LYS ILE ALA VAL ASP ASN ALA ALA GLY SEQRES 33 B 556 PRO TYR GLN ASN HIS THR VAL VAL PHE LEU GLY SER GLU SEQRES 34 B 556 LYS GLY ILE ILE LEU LYS PHE LEU ALA ARG ILE GLY SER SEQRES 35 B 556 SER GLY PHE LEU ASN GLY SER LEU PHE LEU GLU GLU MET SEQRES 36 B 556 ASN VAL TYR ASN PRO GLU LYS CYS SER TYR ASP GLY VAL SEQRES 37 B 556 GLU ASP LYS ARG ILE MET GLY MET GLN LEU ASP ARG ALA SEQRES 38 B 556 SER GLY SER LEU TYR VAL ALA PHE SER THR CYS VAL ILE SEQRES 39 B 556 LYS VAL PRO LEU GLY ARG CYS GLU ARG HIS GLY LYS CYS SEQRES 40 B 556 LYS LYS THR CYS ILE ALA SER ARG ASP PRO TYR CYS GLY SEQRES 41 B 556 TRP VAL ARG GLU SER GLY SER CYS ALA HIS LEU SER PRO SEQRES 42 B 556 LEU SER ARG LEU THR PHE GLU GLN ASP ILE GLU ARG GLY SEQRES 43 B 556 ASN THR ASP GLY LEU GLY ASP CYS HIS ASN MODRES 3AFC ASN B 282 ASN GLYCOSYLATION SITE MODRES 3AFC ASN A 282 ASN GLYCOSYLATION SITE MODRES 3AFC ASN B 434 ASN GLYCOSYLATION SITE MODRES 3AFC ASN A 434 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG A2003 14 HET NAG B2006 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 3 NAG 6(C8 H15 N O6) FORMUL 7 HOH *194(H2 O) HELIX 1 1 HIS A 31 LYS A 36 1 6 HELIX 2 2 ARG A 100 LYS A 110 1 11 HELIX 3 3 HIS A 113 CYS A 117 5 5 HELIX 4 4 MET A 332 PHE A 339 1 8 HELIX 5 5 PRO A 357 VAL A 361 5 5 HELIX 6 6 THR A 380 PHE A 384 5 5 HELIX 7 7 PRO A 385 HIS A 395 1 11 HELIX 8 8 SER A 404 ARG A 408 5 5 HELIX 9 9 ASN A 473 SER A 478 1 6 HELIX 10 10 ARG A 514 GLY A 519 5 6 HELIX 11 11 CYS A 521 SER A 528 1 8 HELIX 12 12 HIS B 31 LYS B 36 1 6 HELIX 13 13 ARG B 100 MET B 109 1 10 HELIX 14 14 HIS B 113 CYS B 117 5 5 HELIX 15 15 VAL B 241 ASN B 244 5 4 HELIX 16 16 MET B 332 PHE B 339 1 8 HELIX 17 17 PRO B 357 VAL B 361 5 5 HELIX 18 18 THR B 380 PHE B 384 5 5 HELIX 19 19 PRO B 385 HIS B 395 1 11 HELIX 20 20 ILE B 454 GLY B 458 5 5 HELIX 21 21 ASN B 473 SER B 478 1 6 SHEET 1 A 5 SER A 28 SER A 30 0 SHEET 2 A 5 LEU A 464 ASN A 470 1 O GLU A 468 N SER A 30 SHEET 3 A 5 ILE A 446 ALA A 452 -1 N ILE A 447 O MET A 469 SHEET 4 A 5 HIS A 435 SER A 442 -1 N VAL A 438 O PHE A 450 SHEET 5 A 5 LEU A 420 ALA A 429 -1 N ALA A 424 O PHE A 439 SHEET 1 B 5 GLU A 88 ILE A 89 0 SHEET 2 B 5 VAL A 40 PHE A 41 1 N VAL A 40 O ILE A 89 SHEET 3 B 5 VAL A 507 PRO A 511 -1 O VAL A 507 N PHE A 41 SHEET 4 B 5 SER A 498 ALA A 502 -1 N LEU A 499 O VAL A 510 SHEET 5 B 5 GLY A 489 ASP A 493 -1 N GLY A 489 O ALA A 502 SHEET 1 C 4 MET A 60 MET A 64 0 SHEET 2 C 4 THR A 67 ALA A 71 -1 O TYR A 69 N MET A 62 SHEET 3 C 4 HIS A 75 ASP A 80 -1 O VAL A 79 N LEU A 68 SHEET 4 C 4 LYS A 93 THR A 96 -1 O LEU A 95 N ILE A 76 SHEET 1 D 4 ILE A 121 LYS A 126 0 SHEET 2 D 4 THR A 131 GLY A 136 -1 O PHE A 133 N LEU A 125 SHEET 3 D 4 SER A 143 ARG A 148 -1 O TYR A 147 N LEU A 132 SHEET 4 D 4 THR A 154 SER A 160 -1 O PHE A 159 N CYS A 144 SHEET 1 E 4 ILE A 174 ALA A 178 0 SHEET 2 E 4 LYS A 181 VAL A 187 -1 O TYR A 183 N LEU A 176 SHEET 3 E 4 ALA A 195 SER A 200 -1 O TYR A 198 N SER A 184 SHEET 4 E 4 LEU A 207 ARG A 208 -1 O LEU A 207 N ARG A 199 SHEET 1 F 4 TYR A 221 TYR A 228 0 SHEET 2 F 4 TYR A 231 ILE A 239 -1 O ARG A 237 N TYR A 221 SHEET 3 F 4 VAL A 250 CYS A 258 -1 O ARG A 253 N PHE A 236 SHEET 4 F 4 LEU A 277 ARG A 280 -1 O LEU A 277 N GLN A 256 SHEET 1 G 2 SER A 284 VAL A 285 0 SHEET 2 G 2 PHE A 291 TYR A 292 -1 O PHE A 291 N VAL A 285 SHEET 1 H 3 ILE A 295 VAL A 299 0 SHEET 2 H 3 ARG A 308 SER A 316 -1 O THR A 314 N GLN A 297 SHEET 3 H 3 ILE A 303 ILE A 305 -1 N ILE A 305 O ARG A 308 SHEET 1 I 4 ILE A 295 VAL A 299 0 SHEET 2 I 4 ARG A 308 SER A 316 -1 O THR A 314 N GLN A 297 SHEET 3 I 4 SER A 325 ASP A 331 -1 O TYR A 330 N VAL A 311 SHEET 4 I 4 PHE A 411 ARG A 413 -1 O ARG A 413 N SER A 325 SHEET 1 J 2 LYS A 344 GLN A 346 0 SHEET 2 J 2 TRP A 353 PRO A 355 -1 O THR A 354 N GLU A 345 SHEET 1 K 3 SER A 541 HIS A 544 0 SHEET 2 K 3 CYS A 533 VAL A 536 -1 N VAL A 536 O SER A 541 SHEET 3 K 3 PHE A 553 GLU A 554 -1 O GLU A 554 N TRP A 535 SHEET 1 L 5 ILE B 29 SER B 30 0 SHEET 2 L 5 LEU B 464 ASN B 470 1 O GLU B 468 N SER B 30 SHEET 3 L 5 ILE B 446 LEU B 451 -1 N ILE B 447 O MET B 469 SHEET 4 L 5 HIS B 435 SER B 442 -1 N LEU B 440 O LEU B 448 SHEET 5 L 5 LEU B 420 ALA B 429 -1 N ALA B 424 O PHE B 439 SHEET 1 M 4 VAL B 40 PHE B 41 0 SHEET 2 M 4 VAL B 507 PRO B 511 -1 O VAL B 507 N PHE B 41 SHEET 3 M 4 SER B 498 ALA B 502 -1 N LEU B 499 O VAL B 510 SHEET 4 M 4 GLY B 489 ASP B 493 -1 N GLY B 489 O ALA B 502 SHEET 1 N 4 MET B 60 MET B 64 0 SHEET 2 N 4 THR B 67 ALA B 71 -1 O TYR B 69 N MET B 62 SHEET 3 N 4 HIS B 75 ASP B 80 -1 O TYR B 77 N VAL B 70 SHEET 4 N 4 LYS B 93 THR B 96 -1 O LEU B 95 N ILE B 76 SHEET 1 O 4 ILE B 121 ASN B 128 0 SHEET 2 O 4 THR B 131 GLY B 136 -1 O PHE B 133 N LEU B 125 SHEET 3 O 4 SER B 143 ARG B 148 -1 O ARG B 145 N VAL B 134 SHEET 4 O 4 THR B 154 SER B 160 -1 O PHE B 159 N CYS B 144 SHEET 1 P 4 ILE B 174 ALA B 178 0 SHEET 2 P 4 LYS B 181 VAL B 187 -1 O TYR B 183 N LEU B 176 SHEET 3 P 4 ALA B 195 SER B 200 -1 O VAL B 196 N THR B 186 SHEET 4 P 4 LEU B 207 ARG B 208 -1 O LEU B 207 N ARG B 199 SHEET 1 Q 4 TYR B 221 TYR B 228 0 SHEET 2 Q 4 TYR B 231 ILE B 239 -1 O PHE B 235 N GLN B 224 SHEET 3 Q 4 VAL B 250 CYS B 258 -1 O ALA B 255 N PHE B 234 SHEET 4 Q 4 LEU B 277 ARG B 280 -1 O LEU B 277 N GLN B 256 SHEET 1 R 2 SER B 284 VAL B 285 0 SHEET 2 R 2 PHE B 291 TYR B 292 -1 O PHE B 291 N VAL B 285 SHEET 1 S 3 ILE B 295 VAL B 299 0 SHEET 2 S 3 ARG B 308 SER B 316 -1 O THR B 314 N GLN B 297 SHEET 3 S 3 ILE B 303 ILE B 305 -1 N ILE B 303 O VAL B 310 SHEET 1 T 4 ILE B 295 VAL B 299 0 SHEET 2 T 4 ARG B 308 SER B 316 -1 O THR B 314 N GLN B 297 SHEET 3 T 4 SER B 325 ASP B 331 -1 O ALA B 326 N PHE B 315 SHEET 4 T 4 PHE B 411 ARG B 413 -1 O ARG B 413 N SER B 325 SHEET 1 U 2 LYS B 344 GLU B 345 0 SHEET 2 U 2 THR B 354 PRO B 355 -1 O THR B 354 N GLU B 345 SSBOND 1 CYS A 107 CYS A 117 1555 1555 2.04 SSBOND 2 CYS A 135 CYS A 144 1555 1555 2.06 SSBOND 3 CYS A 258 CYS A 369 1555 1555 2.05 SSBOND 4 CYS A 283 CYS A 328 1555 1555 2.08 SSBOND 5 CYS A 477 CYS A 506 1555 1555 2.04 SSBOND 6 CYS A 515 CYS A 533 1555 1555 2.03 SSBOND 7 CYS A 521 CYS A 568 1555 1555 2.04 SSBOND 8 CYS A 525 CYS A 542 1555 1555 2.05 SSBOND 9 CYS B 107 CYS B 117 1555 1555 2.06 SSBOND 10 CYS B 135 CYS B 144 1555 1555 2.04 SSBOND 11 CYS B 258 CYS B 369 1555 1555 2.05 SSBOND 12 CYS B 283 CYS B 328 1555 1555 2.08 SSBOND 13 CYS B 477 CYS B 506 1555 1555 2.03 SSBOND 14 CYS B 515 CYS B 533 1555 1555 2.04 LINK ND2 ASN A 282 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 434 C1 NAG A2003 1555 1555 1.46 LINK ND2 ASN B 282 C1 NAG D 1 1555 1555 1.43 LINK ND2 ASN B 434 C1 NAG B2006 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 CISPEP 1 LYS A 363 PRO A 364 0 0.62 CISPEP 2 LYS B 363 PRO B 364 0 -1.73 CRYST1 71.474 89.060 95.523 90.00 102.20 90.00 P 1 21 1 4 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 0.013991 0.000000 0.003026 0.00000 SCALE2 0.000000 0.011228 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010711 0.00000