HEADER PROTEIN BINDING 30-MAR-14 3WSX TITLE SORLA VPS10P DOMAIN IN LIGAND-FREE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTILIN-RELATED RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, UNP RESIDUES 29-753; COMPND 5 SYNONYM: NEURONAL EXTRACELLULAR RECEPTOR; COMPND 6 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 KEYWDS BETA-PROPELLER, RECEPTOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.KITAGO,Z.NAKATA,M.NAGAE,T.NOGI,J.TAKAGI REVDAT 5 20-NOV-24 3WSX 1 REMARK REVDAT 4 08-NOV-23 3WSX 1 HETSYN REVDAT 3 29-JUL-20 3WSX 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 01-JAN-20 3WSX 1 JRNL SEQADV LINK REVDAT 1 04-FEB-15 3WSX 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. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : -1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 53349 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2849 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3910 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 195 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4830 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.525 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5037 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6812 ; 1.654 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 597 ; 6.695 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;32.760 ;23.745 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 798 ;14.022 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;17.549 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 721 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3849 ; 0.008 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3WSX 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_1000096751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56199 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.370 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: 3F6K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 1.2M SODIUM REMARK 280 DIHYDROGEN PHOSPHATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 96.76067 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 193.52133 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 145.14100 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 241.90167 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 48.38033 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 96.76067 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 193.52133 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 241.90167 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 145.14100 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 48.38033 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 29 REMARK 465 VAL A 30 REMARK 465 TRP A 31 REMARK 465 THR A 32 REMARK 465 GLN A 33 REMARK 465 ARG A 34 REMARK 465 LEU A 35 REMARK 465 HIS A 36 REMARK 465 GLY A 37 REMARK 465 GLY A 38 REMARK 465 SER A 39 REMARK 465 ALA A 40 REMARK 465 PRO A 41 REMARK 465 LEU A 42 REMARK 465 PRO A 43 REMARK 465 GLN A 44 REMARK 465 ASP A 45 REMARK 465 ARG A 46 REMARK 465 GLY A 47 REMARK 465 PHE A 48 REMARK 465 LEU A 49 REMARK 465 VAL A 50 REMARK 465 VAL A 51 REMARK 465 GLN A 52 REMARK 465 GLY A 53 REMARK 465 ASP A 54 REMARK 465 PRO A 55 REMARK 465 ARG A 56 REMARK 465 GLU A 57 REMARK 465 LEU A 58 REMARK 465 ARG A 59 REMARK 465 LEU A 60 REMARK 465 TRP A 61 REMARK 465 ALA A 62 REMARK 465 ARG A 63 REMARK 465 GLY A 64 REMARK 465 ASP A 65 REMARK 465 ALA A 66 REMARK 465 ARG A 67 REMARK 465 GLY A 68 REMARK 465 ALA A 69 REMARK 465 SER A 70 REMARK 465 ARG A 71 REMARK 465 ALA A 72 REMARK 465 ASP A 73 REMARK 465 GLU A 74 REMARK 465 LYS A 75 REMARK 465 PRO A 76 REMARK 465 LEU A 77 REMARK 465 ARG A 78 REMARK 465 ARG A 79 REMARK 465 LYS A 80 REMARK 465 ARG A 81 REMARK 465 SER A 82 REMARK 465 ALA A 83 REMARK 465 ALA A 84 REMARK 465 LEU A 85 REMARK 465 GLN A 86 REMARK 465 PRO A 87 REMARK 465 GLU A 88 REMARK 465 LEU A 125 REMARK 465 ALA A 126 REMARK 465 LEU A 127 REMARK 465 ALA A 128 REMARK 465 ARG A 129 REMARK 465 LEU A 315 REMARK 465 LEU A 316 REMARK 465 GLY A 317 REMARK 465 SER A 318 REMARK 465 GLU A 319 REMARK 465 ASN A 430 REMARK 465 GLY A 431 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 ALA A 457 REMARK 465 PHE A 458 REMARK 465 THR A 459 REMARK 465 GLY A 460 REMARK 465 TYR A 461 REMARK 465 GLY A 462 REMARK 465 GLU A 463 REMARK 465 LYS A 464 REMARK 465 ILE A 465 REMARK 465 ASN A 466 REMARK 465 CYS A 467 REMARK 465 GLU A 468 REMARK 465 LEU A 469 REMARK 465 SER A 470 REMARK 465 GLN A 471 REMARK 465 ARG A 480 REMARK 465 LEU A 481 REMARK 465 SER A 482 REMARK 465 GLN A 483 REMARK 465 LEU A 484 REMARK 465 LEU A 485 REMARK 465 ASN A 486 REMARK 465 LEU A 487 REMARK 465 GLN A 488 REMARK 465 LEU A 489 REMARK 465 ARG A 490 REMARK 465 ARG A 491 REMARK 465 ASN A 513 REMARK 465 LEU A 514 REMARK 465 ALA A 515 REMARK 465 SER A 516 REMARK 465 LYS A 604 REMARK 465 GLU A 605 REMARK 465 ASN A 606 REMARK 465 VAL A 607 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 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 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 O ASP A 235 NH2 ARG A 726 6665 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 643 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 654 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 726 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 726 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 744 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES 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 LYS A 113 32.43 -96.55 REMARK 500 ASP A 173 104.66 -161.59 REMARK 500 ASP A 192 48.42 -144.67 REMARK 500 LYS A 229 71.30 54.30 REMARK 500 ASP A 304 -128.83 65.10 REMARK 500 ASP A 353 145.59 -173.08 REMARK 500 ALA A 354 28.98 -148.82 REMARK 500 SER A 364 143.57 79.54 REMARK 500 HIS A 365 27.94 -140.23 REMARK 500 SER A 609 119.34 -161.20 REMARK 500 ASN A 641 109.37 -54.90 REMARK 500 GLU A 642 33.27 -96.38 REMARK 500 SER A 720 -165.37 70.40 REMARK 500 THR A 721 78.20 -113.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 744 LEU A 745 140.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WSY RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEX WITH ITS OWN PROPEPTIDE FRAGMENT REMARK 900 RELATED ID: 3WSZ RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEX WITH ABETA-DERIVED PEPTIDE DBREF 3WSX A 29 753 UNP Q92673 SORL_HUMAN 29 753 SEQADV 3WSX SER A 754 UNP Q92673 EXPRESSION TAG SEQADV 3WSX ARG A 755 UNP Q92673 EXPRESSION TAG SEQADV 3WSX LEU A 756 UNP Q92673 EXPRESSION TAG SEQADV 3WSX GLU A 757 UNP Q92673 EXPRESSION TAG SEQADV 3WSX ASN A 758 UNP Q92673 EXPRESSION TAG SEQADV 3WSX LEU A 759 UNP Q92673 EXPRESSION TAG SEQADV 3WSX TYR A 760 UNP Q92673 EXPRESSION TAG SEQADV 3WSX PHE A 761 UNP Q92673 EXPRESSION TAG SEQADV 3WSX GLN A 762 UNP Q92673 EXPRESSION TAG SEQRES 1 A 734 GLU VAL TRP THR GLN ARG LEU HIS GLY GLY SER ALA PRO SEQRES 2 A 734 LEU PRO GLN ASP ARG GLY PHE LEU VAL VAL GLN GLY ASP SEQRES 3 A 734 PRO ARG GLU LEU ARG LEU TRP ALA ARG GLY ASP ALA ARG SEQRES 4 A 734 GLY ALA SER ARG ALA ASP GLU LYS PRO LEU ARG ARG LYS SEQRES 5 A 734 ARG SER ALA ALA LEU GLN PRO GLU PRO ILE LYS VAL TYR SEQRES 6 A 734 GLY GLN VAL SER LEU ASN ASP SER HIS ASN GLN MET VAL SEQRES 7 A 734 VAL HIS TRP ALA GLY GLU LYS SER ASN VAL ILE VAL ALA SEQRES 8 A 734 LEU ALA ARG ASP SER LEU ALA LEU ALA ARG PRO LYS SER SEQRES 9 A 734 SER ASP VAL TYR VAL SER TYR ASP TYR GLY LYS SER PHE SEQRES 10 A 734 LYS LYS ILE SER ASP LYS LEU ASN PHE GLY LEU GLY ASN SEQRES 11 A 734 ARG SER GLU ALA VAL ILE ALA GLN PHE TYR HIS SER PRO SEQRES 12 A 734 ALA ASP ASN LYS ARG TYR ILE PHE ALA ASP ALA TYR ALA SEQRES 13 A 734 GLN TYR LEU TRP ILE THR PHE ASP PHE CYS ASN THR LEU SEQRES 14 A 734 GLN GLY PHE SER ILE PRO PHE ARG ALA ALA ASP LEU LEU SEQRES 15 A 734 LEU HIS SER LYS ALA SER ASN LEU LEU LEU GLY PHE ASP SEQRES 16 A 734 ARG SER HIS PRO ASN LYS GLN LEU TRP LYS SER ASP ASP SEQRES 17 A 734 PHE GLY GLN THR TRP ILE MET ILE GLN GLU HIS VAL LYS SEQRES 18 A 734 SER PHE SER TRP GLY ILE ASP PRO TYR ASP LYS PRO ASN SEQRES 19 A 734 THR ILE TYR ILE GLU ARG HIS GLU PRO SER GLY TYR SER SEQRES 20 A 734 THR VAL PHE ARG SER THR ASP PHE PHE GLN SER ARG GLU SEQRES 21 A 734 ASN GLN GLU VAL ILE LEU GLU GLU VAL ARG ASP PHE GLN SEQRES 22 A 734 LEU ARG ASP LYS TYR MET PHE ALA THR LYS VAL VAL HIS SEQRES 23 A 734 LEU LEU GLY SER GLU GLN GLN SER SER VAL GLN LEU TRP SEQRES 24 A 734 VAL SER PHE GLY ARG LYS PRO MET ARG ALA ALA GLN PHE SEQRES 25 A 734 VAL THR ARG HIS PRO ILE ASN GLU TYR TYR ILE ALA ASP SEQRES 26 A 734 ALA SER GLU ASP GLN VAL PHE VAL CYS VAL SER HIS SER SEQRES 27 A 734 ASN ASN ARG THR ASN LEU TYR ILE SER GLU ALA GLU GLY SEQRES 28 A 734 LEU LYS PHE SER LEU SER LEU GLU ASN VAL LEU TYR TYR SEQRES 29 A 734 SER PRO GLY GLY ALA GLY SER ASP THR LEU VAL ARG TYR SEQRES 30 A 734 PHE ALA ASN GLU PRO PHE ALA ASP PHE HIS ARG VAL GLU SEQRES 31 A 734 GLY LEU GLN GLY VAL TYR ILE ALA THR LEU ILE ASN GLY SEQRES 32 A 734 SER MET ASN GLU GLU ASN MET ARG SER VAL ILE THR PHE SEQRES 33 A 734 ASP LYS GLY GLY THR TRP GLU PHE LEU GLN ALA PRO ALA SEQRES 34 A 734 PHE THR GLY TYR GLY GLU LYS ILE ASN CYS GLU LEU SER SEQRES 35 A 734 GLN GLY CYS SER LEU HIS LEU ALA GLN ARG LEU SER GLN SEQRES 36 A 734 LEU LEU ASN LEU GLN LEU ARG ARG MET PRO ILE LEU SER SEQRES 37 A 734 LYS GLU SER ALA PRO GLY LEU ILE ILE ALA THR GLY SER SEQRES 38 A 734 VAL GLY LYS ASN LEU ALA SER LYS THR ASN VAL TYR ILE SEQRES 39 A 734 SER SER SER ALA GLY ALA ARG TRP ARG GLU ALA LEU PRO SEQRES 40 A 734 GLY PRO HIS TYR TYR THR TRP GLY ASP HIS GLY GLY ILE SEQRES 41 A 734 ILE THR ALA ILE ALA GLN GLY MET GLU THR ASN GLU LEU SEQRES 42 A 734 LYS TYR SER THR ASN GLU GLY GLU THR TRP LYS THR PHE SEQRES 43 A 734 ILE PHE SER GLU LYS PRO VAL PHE VAL TYR GLY LEU LEU SEQRES 44 A 734 THR GLU PRO GLY GLU LYS SER THR VAL PHE THR ILE PHE SEQRES 45 A 734 GLY SER ASN LYS GLU ASN VAL HIS SER TRP LEU ILE LEU SEQRES 46 A 734 GLN VAL ASN ALA THR ASP ALA LEU GLY VAL PRO CYS THR SEQRES 47 A 734 GLU ASN ASP TYR LYS LEU TRP SER PRO SER ASP GLU ARG SEQRES 48 A 734 GLY ASN GLU CYS LEU LEU GLY HIS LYS THR VAL PHE LYS SEQRES 49 A 734 ARG ARG THR PRO HIS ALA THR CYS PHE ASN GLY GLU ASP SEQRES 50 A 734 PHE ASP ARG PRO VAL VAL VAL SER ASN CYS SER CYS THR SEQRES 51 A 734 ARG GLU ASP TYR GLU CYS ASP PHE GLY PHE LYS MET SER SEQRES 52 A 734 GLU ASP LEU SER LEU GLU VAL CYS VAL PRO ASP PRO GLU SEQRES 53 A 734 PHE SER GLY LYS SER TYR SER PRO PRO VAL PRO CYS PRO SEQRES 54 A 734 VAL GLY SER THR TYR ARG ARG THR ARG GLY TYR ARG LYS SEQRES 55 A 734 ILE SER GLY ASP THR CYS SER GLY GLY ASP VAL GLU ALA SEQRES 56 A 734 ARG LEU GLU GLY GLU LEU VAL PRO CYS PRO SER ARG LEU SEQRES 57 A 734 GLU ASN LEU TYR PHE GLN MODRES 3WSX ASN A 674 ASN GLYCOSYLATION SITE MODRES 3WSX ASN A 616 ASN GLYCOSYLATION SITE MODRES 3WSX ASN A 158 ASN GLYCOSYLATION SITE HET NAG A 801 14 HET NAG A 802 14 HET NAG A 803 14 HET PO4 A 804 5 HET PO4 A 805 5 HET PO4 A 806 5 HET PO4 A 807 5 HET EDO A 808 4 HET EDO A 809 4 HET EDO A 810 4 HET EDO A 811 4 HET EDO A 812 4 HET EDO A 813 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL 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 HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 5 PO4 4(O4 P 3-) FORMUL 9 EDO 6(C2 H6 O2) FORMUL 15 HOH *150(H2 O) HELIX 1 1 SER A 149 LEU A 152 5 4 HELIX 2 2 SER A 286 GLU A 288 5 3 HELIX 3 3 HIS A 365 ASN A 367 5 3 HELIX 4 4 ASP A 544 GLY A 547 5 4 HELIX 5 5 THR A 618 GLY A 622 5 5 HELIX 6 6 THR A 626 ASN A 628 5 3 HELIX 7 7 CYS A 643 LEU A 645 5 3 HELIX 8 8 THR A 678 GLU A 680 5 3 HELIX 9 9 ASP A 693 GLU A 697 5 5 HELIX 10 10 PRO A 703 SER A 706 5 4 SHEET 1 A 4 LYS A 91 LEU A 98 0 SHEET 2 A 4 TRP A 610 ASN A 616 -1 O TRP A 610 N LEU A 98 SHEET 3 A 4 VAL A 596 SER A 602 -1 N GLY A 601 O LEU A 611 SHEET 4 A 4 PHE A 582 THR A 588 -1 N PHE A 582 O SER A 602 SHEET 1 B 4 GLN A 104 TRP A 109 0 SHEET 2 B 4 ILE A 117 ARG A 122 -1 O ARG A 122 N GLN A 104 SHEET 3 B 4 SER A 133 SER A 138 -1 O TYR A 136 N ALA A 119 SHEET 4 B 4 LYS A 146 LYS A 147 -1 O LYS A 146 N VAL A 137 SHEET 1 C 4 ILE A 164 HIS A 169 0 SHEET 2 C 4 TYR A 177 ASP A 181 -1 O ALA A 180 N GLN A 166 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 ASP A 223 -1 O LEU A 220 N LEU A 210 SHEET 3 D 4 GLN A 230 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 ARG A 268 -1 O TYR A 265 N SER A 252 SHEET 3 E 4 SER A 275 SER A 280 -1 O PHE A 278 N ILE A 266 SHEET 4 E 4 GLN A 290 VAL A 297 -1 O VAL A 297 N SER A 275 SHEET 1 F 4 PHE A 300 ARG A 303 0 SHEET 2 F 4 TYR A 306 VAL A 313 -1 O PHE A 308 N GLN A 301 SHEET 3 F 4 SER A 323 PHE A 330 -1 O TRP A 327 N ALA A 309 SHEET 4 F 4 ARG A 336 ALA A 337 -1 O ARG A 336 N VAL A 328 SHEET 1 G 4 TYR A 350 ASP A 353 0 SHEET 2 G 4 PHE A 360 VAL A 363 -1 O CYS A 362 N TYR A 350 SHEET 3 G 4 ARG A 369 ILE A 374 -1 O TYR A 373 N VAL A 361 SHEET 4 G 4 SER A 383 LEU A 390 -1 O LEU A 386 N LEU A 372 SHEET 1 H 4 PHE A 414 ARG A 416 0 SHEET 2 H 4 TYR A 424 LEU A 428 -1 O ILE A 425 N HIS A 415 SHEET 3 H 4 ARG A 439 THR A 443 -1 O ARG A 439 N LEU A 428 SHEET 4 H 4 GLU A 451 PHE A 452 -1 O GLU A 451 N ILE A 442 SHEET 1 I 4 GLN A 454 ALA A 455 0 SHEET 2 I 4 CYS A 473 GLN A 479 -1 O CYS A 473 N ALA A 455 SHEET 3 I 4 ILE A 504 VAL A 510 -1 O SER A 509 N HIS A 476 SHEET 4 I 4 PRO A 493 LEU A 495 -1 N LEU A 495 O ILE A 505 SHEET 1 J 5 GLN A 454 ALA A 455 0 SHEET 2 J 5 CYS A 473 GLN A 479 -1 O CYS A 473 N ALA A 455 SHEET 3 J 5 ILE A 504 VAL A 510 -1 O SER A 509 N HIS A 476 SHEET 4 J 5 ASN A 519 SER A 523 -1 O TYR A 521 N ALA A 506 SHEET 5 J 5 ARG A 531 PRO A 535 -1 O ALA A 533 N VAL A 520 SHEET 1 K 4 HIS A 538 GLY A 543 0 SHEET 2 K 4 ILE A 548 ALA A 553 -1 O ILE A 552 N TYR A 539 SHEET 3 K 4 GLU A 560 SER A 564 -1 O LYS A 562 N ALA A 551 SHEET 4 K 4 LYS A 572 ILE A 575 -1 O LYS A 572 N TYR A 563 SHEET 1 L 3 TYR A 630 TRP A 633 0 SHEET 2 L 3 HIS A 647 ARG A 654 -1 O PHE A 651 N TRP A 633 SHEET 3 L 3 VAL A 671 ASN A 674 -1 O SER A 673 N LYS A 648 SHEET 1 M 2 TYR A 682 CYS A 684 0 SHEET 2 M 2 TYR A 728 LYS A 730 -1 O ARG A 729 N GLU A 683 SHEET 1 N 2 PHE A 688 MET A 690 0 SHEET 2 N 2 CYS A 699 PRO A 701 -1 O VAL A 700 N LYS A 689 SHEET 1 O 2 TYR A 722 ARG A 724 0 SHEET 2 O 2 GLU A 748 VAL A 750 -1 O GLU A 748 N ARG A 724 SSBOND 1 CYS A 625 CYS A 660 1555 1555 2.11 SSBOND 2 CYS A 643 CYS A 675 1555 1555 2.10 SSBOND 3 CYS A 677 CYS A 736 1555 1555 2.13 SSBOND 4 CYS A 684 CYS A 699 1555 1555 2.08 LINK ND2 ASN A 158 C1 NAG A 801 1555 1555 1.45 LINK ND2 ASN A 616 C1 NAG A 802 1555 1555 1.44 LINK ND2 ASN A 674 C1 NAG A 803 1555 1555 1.44 CISPEP 1 ASP A 256 PRO A 257 0 17.57 CRYST1 126.371 126.371 290.282 90.00 90.00 120.00 P 61 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 0.007913 0.004569 0.000000 0.00000 SCALE2 0.000000 0.009137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003445 0.00000