HEADER PROTEIN BINDING 30-MAR-14 3WSY TITLE SORLA VPS10P DOMAIN IN COMPLEX WITH ITS OWN PROPEPTIDE FRAGMENT 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: PEPTIDE FROM SORTILIN-RELATED RECEPTOR; 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 EXISTS AT THE UPSTREAM OF SORTILIN- SOURCE 19 RELATED RECEPTOR 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 3WSY 1 HETSYN REVDAT 3 29-JUL-20 3WSY 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 01-JAN-20 3WSY 1 JRNL SEQADV LINK REVDAT 1 04-FEB-15 3WSY 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. 3.11 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) : 3.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 28704 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1532 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) : 3.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1484 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5351 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.70000 REMARK 3 B22 (A**2) : -0.70000 REMARK 3 B33 (A**2) : 1.40000 REMARK 3 B12 (A**2) : 0.00000 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): 0.555 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.325 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.219 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.825 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5569 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7556 ; 1.503 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 669 ; 7.069 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 270 ;32.763 ;23.926 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 893 ;16.173 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.089 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 810 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4304 ; 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 3WSY 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_1000096752. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31428 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51000 REMARK 200 FOR SHELL : 3.310 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: 3WSX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CACODYLATE, 1.2M SODIUM ACETATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 79.09300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 79.09300 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.72900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 79.09300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.36450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 79.09300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 109.09350 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 79.09300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.09300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.72900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 79.09300 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 109.09350 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 79.09300 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 36.36450 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: 2980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 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 LYS A 708 REMARK 465 SER A 709 REMARK 465 TYR A 710 REMARK 465 SER A 711 REMARK 465 VAL A 718 REMARK 465 GLY A 719 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 GLY C 53 REMARK 465 ASP C 54 REMARK 465 PRO C 55 REMARK 465 ARG C 56 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 N CYS A 699 OH TYR A 728 1.52 REMARK 500 OE2 GLU A 683 NH2 ARG A 729 1.57 REMARK 500 OD2 ASP A 282 OG SER A 286 1.80 REMARK 500 OG SER A 691 OD1 ASP A 693 1.82 REMARK 500 NH1 ARG A 726 O GLU A 746 1.92 REMARK 500 NH1 ARG A 654 O ALA A 658 1.94 REMARK 500 OD2 ASP A 259 NH2 ARG A 332 1.96 REMARK 500 OD1 ASN A 158 OG SER A 160 2.02 REMARK 500 SG CYS A 699 CE1 TYR A 728 2.05 REMARK 500 ND2 ASN A 519 O PRO A 535 2.09 REMARK 500 OD2 ASP A 192 OG1 THR A 196 2.12 REMARK 500 O ARG A 724 N GLU A 748 2.12 REMARK 500 OH TYR A 630 OD1 ASN A 662 2.14 REMARK 500 OG SER A 499 OE1 GLU A 592 2.15 REMARK 500 CD GLU A 683 NH2 ARG A 729 2.15 REMARK 500 O LEU A 125 O LEU A 127 2.16 REMARK 500 OD2 ASP A 236 OG1 THR A 240 2.17 REMARK 500 N ARG A 724 O GLU A 748 2.18 REMARK 500 OG SER A 329 O LYS A 333 2.18 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 OG1 THR A 659 OG1 THR A 659 6555 2.01 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 LEU C 42 CA - CB - CG ANGL. DEV. = 16.1 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 GLU A 88 128.91 -37.39 REMARK 500 ASN A 115 1.72 82.77 REMARK 500 CYS A 194 3.64 86.34 REMARK 500 ASP A 304 -128.15 58.17 REMARK 500 ASN A 388 38.62 71.35 REMARK 500 ASN A 430 -67.40 -98.52 REMARK 500 ASP A 693 89.16 -67.14 REMARK 500 CYS A 736 150.10 -46.62 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: 3WSZ RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEX WITH ABETA-DERIVED PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS RESIDUE BELONGS TO PROTEIN SEQUENCE, 29TH GLU OF Q92673. DBREF 3WSY A 86 753 UNP Q92673 SORL_HUMAN 86 753 DBREF 3WSY C 42 56 UNP Q92673 SORL_HUMAN 42 56 SEQADV 3WSY GLU A 85 UNP Q92673 SEE REMARK 999 SEQADV 3WSY SER A 754 UNP Q92673 EXPRESSION TAG SEQADV 3WSY ARG A 755 UNP Q92673 EXPRESSION TAG SEQADV 3WSY LEU A 756 UNP Q92673 EXPRESSION TAG SEQADV 3WSY GLU A 757 UNP Q92673 EXPRESSION TAG SEQADV 3WSY ASN A 758 UNP Q92673 EXPRESSION TAG SEQADV 3WSY LEU A 759 UNP Q92673 EXPRESSION TAG SEQADV 3WSY TYR A 760 UNP Q92673 EXPRESSION TAG SEQADV 3WSY PHE A 761 UNP Q92673 EXPRESSION TAG SEQADV 3WSY 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 15 LEU PRO GLN ASP ARG GLY PHE LEU VAL VAL GLN GLY ASP SEQRES 2 C 15 PRO ARG MODRES 3WSY ASN A 674 ASN GLYCOSYLATION SITE MODRES 3WSY ASN A 616 ASN GLYCOSYLATION SITE MODRES 3WSY ASN A 430 ASN GLYCOSYLATION SITE MODRES 3WSY ASN A 158 ASN GLYCOSYLATION SITE MODRES 3WSY ASN A 368 ASN GLYCOSYLATION SITE HET NAG A 801 14 HET NAG A 802 14 HET NAG A 803 14 HET NAG A 804 14 HET NAG A 805 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 5(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 ASN A 434 GLU A 436 5 3 HELIX 4 4 GLU A 468 GLY A 472 5 5 HELIX 5 5 GLN A 479 ASN A 486 1 8 HELIX 6 6 ALA A 617 GLY A 622 1 6 HELIX 7 7 THR A 626 ASN A 628 5 3 HELIX 8 8 SER A 634 GLU A 638 5 5 HELIX 9 9 THR A 678 GLU A 680 5 3 HELIX 10 10 GLY A 739 GLU A 746 1 8 SHEET 1 A 4 LYS A 91 SER A 97 0 SHEET 2 A 4 LEU A 611 ASN A 616 -1 O ILE A 612 N VAL A 96 SHEET 3 A 4 VAL A 596 ASN A 603 -1 N ILE A 599 O LEU A 613 SHEET 4 A 4 VAL A 581 LEU A 587 -1 N LEU A 587 O THR A 598 SHEET 1 B 5 PHE A 145 LYS A 147 0 SHEET 2 B 5 SER A 133 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 121 O ASP A 134 SHEET 4 B 5 GLN A 104 TRP A 109 -1 N HIS A 108 O VAL A 118 SHEET 5 B 5 PHE C 48 VAL C 51 1 O PHE C 48 N MET A 105 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 PHE A 222 N ASP A 208 SHEET 3 D 4 LEU A 231 SER A 234 -1 O TRP A 232 N GLY A 221 SHEET 4 D 4 TRP A 241 GLN A 245 -1 O ILE A 242 N LYS A 233 SHEET 1 E 7 VAL A 248 TRP A 253 0 SHEET 2 E 7 ILE A 264 HIS A 269 -1 O TYR A 265 N SER A 252 SHEET 3 E 7 SER A 275 SER A 280 -1 O THR A 276 N ARG A 268 SHEET 4 E 7 GLN A 290 ARG A 303 -1 O VAL A 297 N SER A 275 SHEET 5 E 7 TYR A 306 VAL A 313 -1 O THR A 310 N ARG A 298 SHEET 6 E 7 SER A 323 PHE A 330 -1 O GLN A 325 N LYS A 311 SHEET 7 E 7 ARG A 336 ALA A 337 -1 O ARG A 336 N VAL A 328 SHEET 1 F 5 GLN A 339 PHE A 340 0 SHEET 2 F 5 LYS A 381 LEU A 386 1 O PHE A 382 N GLN A 339 SHEET 3 F 5 THR A 370 ILE A 374 -1 N LEU A 372 O LEU A 386 SHEET 4 F 5 VAL A 359 HIS A 365 -1 N VAL A 361 O TYR A 373 SHEET 5 F 5 ILE A 346 ALA A 354 -1 N TYR A 350 O CYS A 362 SHEET 1 G 2 TYR A 391 TYR A 392 0 SHEET 2 G 2 PHE A 411 ALA A 412 -1 O PHE A 411 N TYR A 392 SHEET 1 H 4 PHE A 414 ARG A 416 0 SHEET 2 H 4 TYR A 424 ILE A 429 -1 O ILE A 425 N HIS A 415 SHEET 3 H 4 MET A 438 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 3 SER A 474 LEU A 477 0 SHEET 2 I 3 ILE A 504 GLY A 511 -1 O SER A 509 N HIS A 476 SHEET 3 I 3 LEU A 495 SER A 496 -1 N LEU A 495 O ILE A 505 SHEET 1 J 4 SER A 474 LEU A 477 0 SHEET 2 J 4 ILE A 504 GLY A 511 -1 O SER A 509 N HIS A 476 SHEET 3 J 4 ASN A 519 SER A 523 -1 O TYR A 521 N ALA A 506 SHEET 4 J 4 ARG A 531 LEU A 534 -1 O LEU A 534 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 548 N GLY A 543 SHEET 3 K 4 GLU A 560 SER A 564 -1 O SER A 564 N ILE A 549 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 670 ASN A 674 -1 O VAL A 671 N VAL A 650 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 THR A 721 ARG A 724 0 SHEET 2 O 2 GLU A 748 PRO A 751 -1 O GLU A 748 N ARG A 724 SSBOND 1 CYS A 467 CYS A 473 1555 1555 2.07 SSBOND 2 CYS A 625 CYS A 660 1555 1555 2.09 SSBOND 3 CYS A 643 CYS A 675 1555 1555 2.04 SSBOND 4 CYS A 677 CYS A 736 1555 1555 2.02 SSBOND 5 CYS A 684 CYS A 699 1555 1555 2.04 SSBOND 6 CYS A 716 CYS A 752 1555 1555 2.04 LINK ND2 ASN A 158 C1 NAG A 801 1555 1555 1.45 LINK ND2 ASN A 368 C1 NAG A 802 1555 1555 1.45 LINK ND2 ASN A 430 C1 NAG A 803 1555 1555 1.45 LINK ND2 ASN A 616 C1 NAG A 804 1555 1555 1.44 LINK ND2 ASN A 674 C1 NAG A 805 1555 1555 1.43 CISPEP 1 LEU A 156 GLY A 157 0 -7.35 CISPEP 2 ASP A 256 PRO A 257 0 -3.11 CISPEP 3 VAL A 714 PRO A 715 0 -3.15 CRYST1 158.186 158.186 145.458 90.00 90.00 90.00 I 41 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 0.006322 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006322 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006875 0.00000