PDB Short entry for 3WSZ HEADER PROTEIN BINDING 30-MAR-14 3WSZ TITLE SORLA VPS10P DOMAIN IN COMPLEX WITH ABETA-DERIVED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTILIN-RELATED RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, UNP RESIDUES 86-753; COMPND 5 SYNONYM: NEURONAL EXTRACELLULAR RECEPTOR; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 10-MER PEPTIDE; COMPND 9 CHAIN: C; COMPND 10 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: SORL1; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: LEC 3.2.8.1; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: CHO CELLS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PEF; SOURCE 13 MOL_ID: 2; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS BETA-PROPELLER, RECEPTOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.KITAGO,Z.NAKATA,M.NAGAE,T.NOGI,J.TAKAGI REVDAT 4 08-NOV-23 3WSZ 1 HETSYN REVDAT 3 29-JUL-20 3WSZ 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 01-JAN-20 3WSZ 1 JRNL SEQADV LINK REVDAT 1 04-FEB-15 3WSZ 0 JRNL AUTH Y.KITAGO,M.NAGAE,Z.NAKATA,M.YAGI-UTSUMI,S.TAKAGI-NIIDOME, JRNL AUTH 2 E.MIHARA,T.NOGI,K.KATO,J.TAKAGI JRNL TITL STRUCTURAL BASIS FOR AMYLOIDOGENIC PEPTIDE RECOGNITION BY JRNL TITL 2 SORLA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 22 199 2015 JRNL REFN ESSN 1545-9985 JRNL PMID 25643321 JRNL DOI 10.1038/NSMB.2954 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16244 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.274 REMARK 3 R VALUE (WORKING SET) : 0.273 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 816 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 49.0149 - 5.8148 0.99 2731 124 0.2589 0.2667 REMARK 3 2 5.8148 - 4.6165 1.00 2611 132 0.2479 0.2571 REMARK 3 3 4.6165 - 4.0332 1.00 2562 126 0.2637 0.2952 REMARK 3 4 4.0332 - 3.6646 1.00 2509 157 0.3050 0.3367 REMARK 3 5 3.6646 - 3.4020 1.00 2512 141 0.3239 0.3790 REMARK 3 6 3.4020 - 3.2015 1.00 2503 136 0.3314 0.3477 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 99.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 129.9 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 : 0.006 4702 REMARK 3 ANGLE : 1.049 6367 REMARK 3 CHIRALITY : 0.068 689 REMARK 3 PLANARITY : 0.004 812 REMARK 3 DIHEDRAL : 14.279 1688 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3WSZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000096753. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 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) : 0.98 REMARK 200 MONOCHROMATOR : DOUBLE SI 111 CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : THE DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 AND THE K-B MIRROR SYSTEM REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16271 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.770 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: 3WSY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 1.41M SODIUM ACETATE, PH REMARK 280 7.8, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.72867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.36433 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 80.72867 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.36433 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 80.72867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 40.36433 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 80.72867 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.36433 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: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 85 REMARK 465 GLN A 86 REMARK 465 PRO A 87 REMARK 465 ALA A 126 REMARK 465 LEU A 127 REMARK 465 ALA A 128 REMARK 465 ARG A 129 REMARK 465 GLU A 319 REMARK 465 GLN A 320 REMARK 465 GLN A 321 REMARK 465 SER A 322 REMARK 465 SER A 323 REMARK 465 VAL A 324 REMARK 465 GLN A 325 REMARK 465 ALA A 377 REMARK 465 GLU A 378 REMARK 465 GLY A 379 REMARK 465 LEU A 380 REMARK 465 SER A 432 REMARK 465 MET A 433 REMARK 465 ASN A 434 REMARK 465 GLU A 435 REMARK 465 GLU A 436 REMARK 465 TYR A 461 REMARK 465 GLY A 462 REMARK 465 GLU A 463 REMARK 465 LEU A 644 REMARK 465 LEU A 645 REMARK 465 GLY A 646 REMARK 465 HIS A 647 REMARK 465 SER A 676 REMARK 465 CYS A 677 REMARK 465 THR A 678 REMARK 465 ARG A 679 REMARK 465 GLU A 680 REMARK 465 ASP A 681 REMARK 465 TYR A 682 REMARK 465 GLU A 683 REMARK 465 CYS A 684 REMARK 465 ASP A 685 REMARK 465 PHE A 686 REMARK 465 GLY A 687 REMARK 465 PHE A 688 REMARK 465 LYS A 689 REMARK 465 MET A 690 REMARK 465 SER A 691 REMARK 465 GLU A 692 REMARK 465 ASP A 693 REMARK 465 LEU A 694 REMARK 465 SER A 695 REMARK 465 LEU A 696 REMARK 465 GLU A 697 REMARK 465 VAL A 698 REMARK 465 CYS A 699 REMARK 465 VAL A 700 REMARK 465 PRO A 701 REMARK 465 ASP A 702 REMARK 465 PRO A 703 REMARK 465 GLU A 704 REMARK 465 PHE A 705 REMARK 465 SER A 706 REMARK 465 GLY A 707 REMARK 465 LYS A 708 REMARK 465 SER A 709 REMARK 465 TYR A 710 REMARK 465 SER A 711 REMARK 465 PRO A 712 REMARK 465 PRO A 713 REMARK 465 VAL A 714 REMARK 465 PRO A 715 REMARK 465 CYS A 716 REMARK 465 PRO A 717 REMARK 465 VAL A 718 REMARK 465 GLY A 719 REMARK 465 SER A 720 REMARK 465 THR A 721 REMARK 465 TYR A 722 REMARK 465 ARG A 723 REMARK 465 ARG A 724 REMARK 465 THR A 725 REMARK 465 ARG A 726 REMARK 465 GLY A 727 REMARK 465 TYR A 728 REMARK 465 ARG A 729 REMARK 465 LYS A 730 REMARK 465 ILE A 731 REMARK 465 SER A 732 REMARK 465 GLY A 733 REMARK 465 ASP A 734 REMARK 465 THR A 735 REMARK 465 CYS A 736 REMARK 465 SER A 737 REMARK 465 GLY A 738 REMARK 465 GLY A 739 REMARK 465 ASP A 740 REMARK 465 VAL A 741 REMARK 465 GLU A 742 REMARK 465 ALA A 743 REMARK 465 ARG A 744 REMARK 465 LEU A 745 REMARK 465 GLU A 746 REMARK 465 GLY A 747 REMARK 465 GLU A 748 REMARK 465 LEU A 749 REMARK 465 VAL A 750 REMARK 465 PRO A 751 REMARK 465 CYS A 752 REMARK 465 PRO A 753 REMARK 465 SER A 754 REMARK 465 ARG A 755 REMARK 465 LEU A 756 REMARK 465 GLU A 757 REMARK 465 ASN A 758 REMARK 465 LEU A 759 REMARK 465 TYR A 760 REMARK 465 PHE A 761 REMARK 465 GLN A 762 REMARK 465 ALA C 6 REMARK 465 ALA C 7 REMARK 465 ALA C 8 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 490 O ALA C 10 1.94 REMARK 500 ND2 ASN A 519 O PRO A 535 2.12 REMARK 500 ND2 ASN A 430 C2 NAG A 802 2.15 REMARK 500 O PRO A 345 ND1 HIS A 365 2.17 REMARK 500 O SER A 499 NH1 ARG A 668 2.19 REMARK 500 OG1 THR A 443 O ASP A 445 2.19 REMARK 500 OG SER A 634 O THR A 649 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ND2 ASN A 228 O7 NAG A 801 11555 2.14 REMARK 500 OG1 THR A 659 OG1 THR A 659 4565 2.15 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 ASN A 115 34.68 -89.21 REMARK 500 SER A 160 135.35 -35.52 REMARK 500 ASN A 262 -0.02 69.53 REMARK 500 ASP A 304 -126.42 56.01 REMARK 500 ALA A 309 144.03 -171.83 REMARK 500 ASP A 357 -16.91 82.27 REMARK 500 ASN A 430 -81.12 -124.79 REMARK 500 ALA A 526 16.22 58.14 REMARK 500 ASN A 559 19.12 -140.28 REMARK 500 ALA C 10 -91.08 -126.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WSX RELATED DB: PDB REMARK 900 SAME PROTEIN LIGAND-FREE FORM REMARK 900 RELATED ID: 3WSY RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEX WITH ITS OWN PROPEPTIDE FRAGMENT REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS RESIDUE BELONGS TO PROTEIN SEQUENCE, 29TH GLU OF Q92673. DBREF 3WSZ A 86 753 UNP Q92673 SORL_HUMAN 86 753 DBREF 3WSZ C 6 15 PDB 3WSZ 3WSZ 6 15 SEQADV 3WSZ GLU A 85 UNP Q92673 SEE REMARK 999 SEQADV 3WSZ SER A 754 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ ARG A 755 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ LEU A 756 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ GLU A 757 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ ASN A 758 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ LEU A 759 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ TYR A 760 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ PHE A 761 UNP Q92673 EXPRESSION TAG SEQADV 3WSZ GLN A 762 UNP Q92673 EXPRESSION TAG SEQRES 1 A 678 GLU GLN PRO GLU PRO ILE LYS VAL TYR GLY GLN VAL SER SEQRES 2 A 678 LEU ASN ASP SER HIS ASN GLN MET VAL VAL HIS TRP ALA SEQRES 3 A 678 GLY GLU LYS SER ASN VAL ILE VAL ALA LEU ALA ARG ASP SEQRES 4 A 678 SER LEU ALA LEU ALA ARG PRO LYS SER SER ASP VAL TYR SEQRES 5 A 678 VAL SER TYR ASP TYR GLY LYS SER PHE LYS LYS ILE SER SEQRES 6 A 678 ASP LYS LEU ASN PHE GLY LEU GLY ASN ARG SER GLU ALA SEQRES 7 A 678 VAL ILE ALA GLN PHE TYR HIS SER PRO ALA ASP ASN LYS SEQRES 8 A 678 ARG TYR ILE PHE ALA ASP ALA TYR ALA GLN TYR LEU TRP SEQRES 9 A 678 ILE THR PHE ASP PHE CYS ASN THR LEU GLN GLY PHE SER SEQRES 10 A 678 ILE PRO PHE ARG ALA ALA ASP LEU LEU LEU HIS SER LYS SEQRES 11 A 678 ALA SER ASN LEU LEU LEU GLY PHE ASP ARG SER HIS PRO SEQRES 12 A 678 ASN LYS GLN LEU TRP LYS SER ASP ASP PHE GLY GLN THR SEQRES 13 A 678 TRP ILE MET ILE GLN GLU HIS VAL LYS SER PHE SER TRP SEQRES 14 A 678 GLY ILE ASP PRO TYR ASP LYS PRO ASN THR ILE TYR ILE SEQRES 15 A 678 GLU ARG HIS GLU PRO SER GLY TYR SER THR VAL PHE ARG SEQRES 16 A 678 SER THR ASP PHE PHE GLN SER ARG GLU ASN GLN GLU VAL SEQRES 17 A 678 ILE LEU GLU GLU VAL ARG ASP PHE GLN LEU ARG ASP LYS SEQRES 18 A 678 TYR MET PHE ALA THR LYS VAL VAL HIS LEU LEU GLY SER SEQRES 19 A 678 GLU GLN GLN SER SER VAL GLN LEU TRP VAL SER PHE GLY SEQRES 20 A 678 ARG LYS PRO MET ARG ALA ALA GLN PHE VAL THR ARG HIS SEQRES 21 A 678 PRO ILE ASN GLU TYR TYR ILE ALA ASP ALA SER GLU ASP SEQRES 22 A 678 GLN VAL PHE VAL CYS VAL SER HIS SER ASN ASN ARG THR SEQRES 23 A 678 ASN LEU TYR ILE SER GLU ALA GLU GLY LEU LYS PHE SER SEQRES 24 A 678 LEU SER LEU GLU ASN VAL LEU TYR TYR SER PRO GLY GLY SEQRES 25 A 678 ALA GLY SER ASP THR LEU VAL ARG TYR PHE ALA ASN GLU SEQRES 26 A 678 PRO PHE ALA ASP PHE HIS ARG VAL GLU GLY LEU GLN GLY SEQRES 27 A 678 VAL TYR ILE ALA THR LEU ILE ASN GLY SER MET ASN GLU SEQRES 28 A 678 GLU ASN MET ARG SER VAL ILE THR PHE ASP LYS GLY GLY SEQRES 29 A 678 THR TRP GLU PHE LEU GLN ALA PRO ALA PHE THR GLY TYR SEQRES 30 A 678 GLY GLU LYS ILE ASN CYS GLU LEU SER GLN GLY CYS SER SEQRES 31 A 678 LEU HIS LEU ALA GLN ARG LEU SER GLN LEU LEU ASN LEU SEQRES 32 A 678 GLN LEU ARG ARG MET PRO ILE LEU SER LYS GLU SER ALA SEQRES 33 A 678 PRO GLY LEU ILE ILE ALA THR GLY SER VAL GLY LYS ASN SEQRES 34 A 678 LEU ALA SER LYS THR ASN VAL TYR ILE SER SER SER ALA SEQRES 35 A 678 GLY ALA ARG TRP ARG GLU ALA LEU PRO GLY PRO HIS TYR SEQRES 36 A 678 TYR THR TRP GLY ASP HIS GLY GLY ILE ILE THR ALA ILE SEQRES 37 A 678 ALA GLN GLY MET GLU THR ASN GLU LEU LYS TYR SER THR SEQRES 38 A 678 ASN GLU GLY GLU THR TRP LYS THR PHE ILE PHE SER GLU SEQRES 39 A 678 LYS PRO VAL PHE VAL TYR GLY LEU LEU THR GLU PRO GLY SEQRES 40 A 678 GLU LYS SER THR VAL PHE THR ILE PHE GLY SER ASN LYS SEQRES 41 A 678 GLU ASN VAL HIS SER TRP LEU ILE LEU GLN VAL ASN ALA SEQRES 42 A 678 THR ASP ALA LEU GLY VAL PRO CYS THR GLU ASN ASP TYR SEQRES 43 A 678 LYS LEU TRP SER PRO SER ASP GLU ARG GLY ASN GLU CYS SEQRES 44 A 678 LEU LEU GLY HIS LYS THR VAL PHE LYS ARG ARG THR PRO SEQRES 45 A 678 HIS ALA THR CYS PHE ASN GLY GLU ASP PHE ASP ARG PRO SEQRES 46 A 678 VAL VAL VAL SER ASN CYS SER CYS THR ARG GLU ASP TYR SEQRES 47 A 678 GLU CYS ASP PHE GLY PHE LYS MET SER GLU ASP LEU SER SEQRES 48 A 678 LEU GLU VAL CYS VAL PRO ASP PRO GLU PHE SER GLY LYS SEQRES 49 A 678 SER TYR SER PRO PRO VAL PRO CYS PRO VAL GLY SER THR SEQRES 50 A 678 TYR ARG ARG THR ARG GLY TYR ARG LYS ILE SER GLY ASP SEQRES 51 A 678 THR CYS SER GLY GLY ASP VAL GLU ALA ARG LEU GLU GLY SEQRES 52 A 678 GLU LEU VAL PRO CYS PRO SER ARG LEU GLU ASN LEU TYR SEQRES 53 A 678 PHE GLN SEQRES 1 C 10 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA MODRES 3WSZ ASN A 158 ASN GLYCOSYLATION SITE MODRES 3WSZ ASN A 430 ASN GLYCOSYLATION SITE MODRES 3WSZ ASN A 674 ASN GLYCOSYLATION SITE MODRES 3WSZ ASN A 616 ASN GLYCOSYLATION SITE HET NAG A 801 14 HET NAG A 802 14 HET NAG A 803 14 HET NAG A 804 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 4(C8 H15 N O6) HELIX 1 1 SER A 149 LEU A 152 5 4 HELIX 2 2 THR A 401 PHE A 406 5 6 HELIX 3 3 GLN A 479 ASN A 486 1 8 HELIX 4 4 ALA A 617 GLY A 622 1 6 HELIX 5 5 THR A 626 ASN A 628 5 3 HELIX 6 6 SER A 634 ARG A 639 1 6 SHEET 1 A 4 LYS A 91 VAL A 96 0 SHEET 2 A 4 TRP A 610 ASN A 616 -1 O ASN A 616 N LYS A 91 SHEET 3 A 4 VAL A 596 SER A 602 -1 N ILE A 599 O LEU A 613 SHEET 4 A 4 PHE A 582 LEU A 587 -1 N LEU A 587 O THR A 598 SHEET 1 B 5 LYS A 146 LYS A 147 0 SHEET 2 B 5 ASP A 134 SER A 138 -1 N VAL A 137 O LYS A 146 SHEET 3 B 5 ILE A 117 ARG A 122 -1 N ALA A 119 O TYR A 136 SHEET 4 B 5 GLN A 104 TRP A 109 -1 N HIS A 108 O VAL A 118 SHEET 5 B 5 ALA C 12 ALA C 13 1 O ALA C 13 N VAL A 107 SHEET 1 C 4 ILE A 164 HIS A 169 0 SHEET 2 C 4 TYR A 177 ASP A 181 -1 O ILE A 178 N TYR A 168 SHEET 3 C 4 TYR A 186 THR A 190 -1 O TRP A 188 N PHE A 179 SHEET 4 C 4 GLN A 198 SER A 201 -1 O PHE A 200 N LEU A 187 SHEET 1 D 4 ASP A 208 LEU A 211 0 SHEET 2 D 4 LEU A 219 PHE A 222 -1 O LEU A 220 N LEU A 210 SHEET 3 D 4 LEU A 231 SER A 234 -1 O TRP A 232 N GLY A 221 SHEET 4 D 4 ILE A 242 GLN A 245 -1 O GLN A 245 N LEU A 231 SHEET 1 E 4 VAL A 248 TRP A 253 0 SHEET 2 E 4 ILE A 264 HIS A 269 -1 O GLU A 267 N LYS A 249 SHEET 3 E 4 SER A 275 SER A 280 -1 O PHE A 278 N ILE A 266 SHEET 4 E 4 GLU A 291 VAL A 292 -1 O GLU A 291 N ARG A 279 SHEET 1 F 4 ASP A 299 ARG A 303 0 SHEET 2 F 4 TYR A 306 THR A 310 -1 O PHE A 308 N GLN A 301 SHEET 3 F 4 TRP A 327 PHE A 330 -1 O TRP A 327 N ALA A 309 SHEET 4 F 4 LYS A 333 ALA A 337 -1 O ARG A 336 N VAL A 328 SHEET 1 G 4 ILE A 346 SER A 355 0 SHEET 2 G 4 GLN A 358 HIS A 365 -1 O CYS A 362 N TYR A 350 SHEET 3 G 4 THR A 370 ILE A 374 -1 O ASN A 371 N VAL A 363 SHEET 4 G 4 SER A 383 GLU A 387 -1 O LEU A 386 N LEU A 372 SHEET 1 H 2 TYR A 391 TYR A 392 0 SHEET 2 H 2 PHE A 411 ALA A 412 -1 O PHE A 411 N TYR A 392 SHEET 1 I 4 PHE A 414 ARG A 416 0 SHEET 2 I 4 TYR A 424 ILE A 429 -1 O ILE A 425 N HIS A 415 SHEET 3 I 4 MET A 438 THR A 443 -1 O ARG A 439 N LEU A 428 SHEET 4 I 4 GLU A 451 PHE A 452 -1 O GLU A 451 N ILE A 442 SHEET 1 J 3 SER A 474 ALA A 478 0 SHEET 2 J 3 ILE A 504 GLY A 511 -1 O SER A 509 N HIS A 476 SHEET 3 J 3 LEU A 495 SER A 496 -1 N LEU A 495 O ILE A 505 SHEET 1 K 4 SER A 474 ALA A 478 0 SHEET 2 K 4 ILE A 504 GLY A 511 -1 O SER A 509 N HIS A 476 SHEET 3 K 4 ASN A 519 SER A 523 -1 O TYR A 521 N ALA A 506 SHEET 4 K 4 ARG A 531 LEU A 534 -1 O LEU A 534 N VAL A 520 SHEET 1 L 4 HIS A 538 GLY A 543 0 SHEET 2 L 4 ILE A 548 ALA A 553 -1 O ILE A 552 N TYR A 539 SHEET 3 L 4 GLU A 560 SER A 564 -1 O LYS A 562 N ALA A 551 SHEET 4 L 4 LYS A 572 ILE A 575 -1 O PHE A 574 N LEU A 561 SHEET 1 M 3 TYR A 630 TRP A 633 0 SHEET 2 M 3 THR A 649 ARG A 654 -1 O PHE A 651 N TRP A 633 SHEET 3 M 3 VAL A 670 VAL A 672 -1 O VAL A 671 N VAL A 650 SSBOND 1 CYS A 467 CYS A 473 1555 1555 2.03 SSBOND 2 CYS A 625 CYS A 660 1555 1555 2.04 SSBOND 3 CYS A 643 CYS A 675 1555 1555 2.03 LINK ND2 ASN A 158 C1 NAG A 801 1555 1555 1.45 LINK ND2 ASN A 430 C1 NAG A 802 1555 1555 1.45 LINK ND2 ASN A 616 C1 NAG A 803 1555 1555 1.46 LINK ND2 ASN A 674 C1 NAG A 804 1555 1555 1.46 CISPEP 1 ASP A 256 PRO A 257 0 4.67 CISPEP 2 GLY A 395 GLY A 396 0 -0.07 CISPEP 3 GLU A 605 ASN A 606 0 3.02 CISPEP 4 GLY A 640 ASN A 641 0 9.19 CRYST1 163.735 163.735 121.093 90.00 90.00 120.00 P 62 2 2 12 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 0.006107 0.003526 0.000000 0.00000 SCALE2 0.000000 0.007052 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008258 0.00000