HEADER CELL ADHESION 15-AUG-18 6EET TITLE CRYSTAL STRUCTURE OF MOUSE PROTOCADHERIN-15 EC9-MAD12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTOCADHERIN-15; COMPND 3 CHAIN: A; COMPND 4 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: PCDH15; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: EXPI293; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PHIS-N1 KEYWDS MECHANOTRANSDUCTION, CALCIUM BINDING PROTEIN, CELL ADHESION, HEARING, KEYWDS 2 STEREOCILIA, TIP LINK EXPDTA X-RAY DIFFRACTION AUTHOR Y.NARUI,M.SOTOMAYOR REVDAT 5 11-OCT-23 6EET 1 REMARK REVDAT 4 07-OCT-20 6EET 1 JRNL HETSYN REVDAT 3 29-JUL-20 6EET 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 18-DEC-19 6EET 1 REMARK REVDAT 1 21-AUG-19 6EET 0 JRNL AUTH D.CHOUDHARY,Y.NARUI,B.L.NEEL,L.N.WIMALASENA,C.F.KLANSECK, JRNL AUTH 2 P.DE-LA-TORRE,C.CHEN,R.ARAYA-SECCHI,E.TAMILSELVAN, JRNL AUTH 3 M.SOTOMAYOR JRNL TITL STRUCTURAL DETERMINANTS OF PROTOCADHERIN-15 MECHANICS AND JRNL TITL 2 FUNCTION IN HEARING AND BALANCE PERCEPTION. JRNL REF PROC.NATL.ACAD.SCI.USA 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32963095 JRNL DOI 10.1073/PNAS.1920444117 REMARK 2 REMARK 2 RESOLUTION. 3.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15743 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 790 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) : 3.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1065 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.4700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3476 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.33000 REMARK 3 B22 (A**2) : 1.90000 REMARK 3 B33 (A**2) : -5.23000 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): 0.922 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.367 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.279 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.838 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3658 ; 0.008 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 3305 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4983 ; 1.397 ; 1.704 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7768 ; 0.809 ; 1.668 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 442 ; 8.228 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 189 ;36.253 ;22.169 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 594 ;18.554 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.287 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 504 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4037 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 633 ; 0.001 ; 0.020 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): 1771 ; 5.993 ; 9.426 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1770 ; 5.974 ; 9.425 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2212 ; 8.767 ;14.138 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2213 ; 8.766 ;14.141 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1884 ; 6.659 ;10.094 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1884 ; 6.650 ;10.094 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2771 ;10.234 ;14.953 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4068 ;12.480 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4068 ;12.486 ; 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 : NULL 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 6EET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V717 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V717 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16630 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5290 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) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.80800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.222 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER V2.7.0 REMARK 200 STARTING MODEL: 6BXZ, 4XHZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM SALT, 30% (W/V) REMARK 280 MPD, 5% (W/V) PEG4000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.76400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.76400 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 1.000000 0.000000 0.000000 64.75350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 85.02950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 64.75350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 85.02950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.76400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 64.75350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 85.02950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.76400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 64.75350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 85.02950 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 MET A 898 REMARK 465 ILE A 1342 REMARK 465 LYS A 1343 REMARK 465 LYS A 1344 REMARK 465 ARG A 1345 REMARK 465 GLY A 1346 REMARK 465 GLU A 1347 REMARK 465 SER A 1348 REMARK 465 LEU A 1349 REMARK 465 GLY A 1350 REMARK 465 TYR A 1351 REMARK 465 THR A 1352 REMARK 465 GLU A 1353 REMARK 465 LYS A 1354 REMARK 465 VAL A 1355 REMARK 465 PRO A 1356 REMARK 465 ARG A 1357 REMARK 465 ALA A 1358 REMARK 465 ARG A 1359 REMARK 465 ASP A 1360 REMARK 465 PRO A 1361 REMARK 465 PRO A 1362 REMARK 465 VAL A 1363 REMARK 465 GLY A 1364 REMARK 465 GLY A 1365 REMARK 465 HIS A 1366 REMARK 465 HIS A 1367 REMARK 465 HIS A 1368 REMARK 465 HIS A 1369 REMARK 465 HIS A 1370 REMARK 465 HIS A 1371 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 OG SER A 998 C2 MAN A 1408 1.92 REMARK 500 OG1 THR A 1000 C2 MAN A 1406 2.19 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 ASP A 900 11.33 -162.98 REMARK 500 ALA A 918 133.52 -38.86 REMARK 500 PRO A 977 156.22 -45.94 REMARK 500 THR A 978 12.48 55.89 REMARK 500 ASP A 989 -177.01 -62.80 REMARK 500 ASP A 990 41.17 -143.87 REMARK 500 ALA A1041 132.64 -174.27 REMARK 500 ASN A1054 50.87 -108.30 REMARK 500 ASN A1071 -77.42 -100.61 REMARK 500 ASP A1075 104.54 -163.26 REMARK 500 THR A1078 -65.08 -91.27 REMARK 500 ASN A1097 45.23 75.45 REMARK 500 VAL A1100 66.30 -119.58 REMARK 500 PHE A1139 24.46 80.38 REMARK 500 ARG A1194 -5.88 82.67 REMARK 500 ASN A1297 -14.39 72.98 REMARK 500 ALA A1299 -176.03 -59.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 943 0.12 SIDE CHAIN REMARK 500 ARG A1020 0.17 SIDE CHAIN REMARK 500 ARG A1137 0.08 SIDE CHAIN REMARK 500 ARG A1161 0.18 SIDE CHAIN REMARK 500 ARG A1193 0.10 SIDE CHAIN REMARK 500 ARG A1272 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1412 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 899 OD1 REMARK 620 2 TYR A 901 O 110.6 REMARK 620 3 ASP A 931 OD1 141.9 94.6 REMARK 620 4 ASP A 931 OD2 159.7 78.0 50.7 REMARK 620 5 ASP A 933 OD2 88.8 80.1 67.3 111.0 REMARK 620 6 ALA A 939 O 89.1 159.6 65.8 84.9 96.1 REMARK 620 7 ASP A 989 OD1 88.1 116.4 106.2 71.7 163.2 67.4 REMARK 620 8 ASP A 989 OD2 67.1 85.0 146.0 96.4 144.9 108.0 46.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1409 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A1026 OE2 REMARK 620 2 GLU A1077 OE1 111.7 REMARK 620 3 GLU A1077 OE2 82.0 45.6 REMARK 620 4 ASP A1115 OD1 90.1 83.7 118.3 REMARK 620 5 GLU A1116 O 80.6 161.2 153.2 82.1 REMARK 620 6 ASP A1118 OD1 85.6 106.3 70.1 170.0 88.2 REMARK 620 7 ASP A1151 OD1 155.1 88.7 104.5 106.9 83.8 74.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1411 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A1026 OE1 REMARK 620 2 ASP A1075 OD1 103.4 REMARK 620 3 GLU A1077 OE2 81.3 91.9 REMARK 620 4 ASP A1118 OD2 95.5 160.5 95.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1410 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A1117 OD1 REMARK 620 2 HIS A1119 O 92.4 REMARK 620 3 ASP A1149 OD1 154.6 62.8 REMARK 620 4 ASP A1151 OD2 90.1 77.8 89.7 REMARK 620 5 TYR A1155 O 91.1 174.0 113.2 107.2 REMARK 620 6 ASP A1205 OD2 82.1 95.5 94.3 169.6 80.1 REMARK 620 N 1 2 3 4 5 DBREF 6EET A 898 1353 UNP Q99PJ1 PCD15_MOUSE 919 1374 SEQADV 6EET LYS A 1354 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET VAL A 1355 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET PRO A 1356 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET ARG A 1357 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET ALA A 1358 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET ARG A 1359 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET ASP A 1360 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET PRO A 1361 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET PRO A 1362 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET VAL A 1363 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET GLY A 1364 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET GLY A 1365 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET HIS A 1366 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET HIS A 1367 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET HIS A 1368 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET HIS A 1369 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET HIS A 1370 UNP Q99PJ1 EXPRESSION TAG SEQADV 6EET HIS A 1371 UNP Q99PJ1 EXPRESSION TAG SEQRES 1 A 474 MET ASN ASP TYR PRO PRO VAL PHE SER LYS ARG ILE TYR SEQRES 2 A 474 LYS GLY MET VAL ALA PRO ASP ALA VAL LYS GLY THR PRO SEQRES 3 A 474 ILE THR THR VAL TYR ALA GLU ASP ALA ASP PRO PRO GLY SEQRES 4 A 474 MET PRO ALA SER ARG VAL ARG TYR ARG VAL ASP ASP VAL SEQRES 5 A 474 GLN PHE PRO TYR PRO ALA SER ILE PHE ASP VAL GLU GLU SEQRES 6 A 474 ASP SER GLY ARG VAL VAL THR ARG VAL ASN LEU ASN GLU SEQRES 7 A 474 GLU PRO THR THR ILE PHE LYS LEU VAL VAL VAL ALA PHE SEQRES 8 A 474 ASP ASP GLY GLU PRO VAL MET SER SER SER ALA THR VAL SEQRES 9 A 474 ARG ILE LEU VAL LEU HIS PRO GLY GLU ILE PRO ARG PHE SEQRES 10 A 474 THR GLN GLU GLU TYR ARG PRO PRO PRO VAL SER GLU LEU SEQRES 11 A 474 ALA ALA ARG GLY THR VAL VAL GLY VAL ILE SER ALA ALA SEQRES 12 A 474 ALA ILE ASN GLN SER ILE VAL TYR SER ILE VAL ALA GLY SEQRES 13 A 474 ASN GLU GLU ASP LYS PHE GLY ILE ASN ASN VAL THR GLY SEQRES 14 A 474 VAL ILE TYR VAL ASN SER PRO LEU ASP TYR GLU THR ARG SEQRES 15 A 474 THR SER TYR VAL LEU ARG VAL GLN ALA ASP SER LEU GLU SEQRES 16 A 474 VAL VAL LEU ALA ASN LEU ARG VAL PRO SER LYS SER ASN SEQRES 17 A 474 THR ALA LYS VAL TYR ILE GLU ILE GLN ASP GLU ASN ASP SEQRES 18 A 474 HIS PRO PRO VAL PHE GLN LYS LYS PHE TYR ILE GLY GLY SEQRES 19 A 474 VAL SER GLU ASP ALA ARG MET PHE ALA SER VAL LEU ARG SEQRES 20 A 474 VAL LYS ALA THR ASP ARG ASP THR GLY ASN TYR SER ALA SEQRES 21 A 474 MET ALA TYR ARG LEU ILE ILE PRO PRO ILE LYS GLU GLY SEQRES 22 A 474 LYS GLU GLY PHE VAL VAL GLU THR TYR THR GLY LEU ILE SEQRES 23 A 474 LYS THR ALA MET LEU PHE HIS ASN MET ARG ARG SER TYR SEQRES 24 A 474 PHE LYS PHE GLN VAL ILE ALA THR ASP ASP TYR GLY LYS SEQRES 25 A 474 GLY LEU SER GLY LYS ALA ASP VAL LEU VAL SER VAL VAL SEQRES 26 A 474 ASN GLN LEU ASP MET GLN VAL ILE VAL SER ASN VAL PRO SEQRES 27 A 474 PRO THR LEU VAL GLU LYS LYS ILE GLU ASP LEU THR GLU SEQRES 28 A 474 ILE LEU ASP ARG TYR VAL GLN GLU GLN ILE PRO GLY ALA SEQRES 29 A 474 LYS VAL VAL VAL GLU SER ILE GLY ALA ARG ARG HIS GLY SEQRES 30 A 474 ASP ALA TYR SER LEU GLU ASP TYR SER LYS CYS ASP LEU SEQRES 31 A 474 THR VAL TYR ALA ILE ASP PRO GLN THR ASN ARG ALA ILE SEQRES 32 A 474 ASP ARG ASN GLU LEU PHE LYS PHE LEU ASP GLY LYS LEU SEQRES 33 A 474 LEU ASP ILE ASN LYS ASP PHE GLN PRO TYR TYR GLY GLU SEQRES 34 A 474 GLY GLY ARG ILE LEU GLU ILE ARG THR PRO GLU ALA VAL SEQRES 35 A 474 THR SER ILE LYS LYS ARG GLY GLU SER LEU GLY TYR THR SEQRES 36 A 474 GLU LYS VAL PRO ARG ALA ARG ASP PRO PRO VAL GLY GLY SEQRES 37 A 474 HIS HIS HIS HIS HIS HIS HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET MAN A1405 11 HET MAN A1406 11 HET EPE A1407 15 HET MAN A1408 11 HET CA A1409 1 HET CA A1410 1 HET CA A1411 1 HET CA A1412 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM CA CALCIUM ION 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN EPE HEPES FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 4 MAN 3(C6 H12 O6) FORMUL 6 EPE C8 H18 N2 O4 S FORMUL 8 CA 4(CA 2+) HELIX 1 AA1 MET A 937 ARG A 941 5 5 HELIX 2 AA2 PHE A 951 ILE A 957 1 7 HELIX 3 AA3 HIS A 1007 ILE A 1011 5 5 HELIX 4 AA4 LEU A 1091 ASN A 1097 1 7 HELIX 5 AA5 THR A 1152 ALA A 1157 5 6 HELIX 6 AA6 ILE A 1167 LYS A 1171 5 5 HELIX 7 AA7 ASP A 1205 LYS A 1209 1 5 HELIX 8 AA8 ASN A 1223 MET A 1227 5 5 HELIX 9 AA9 PRO A 1235 LYS A 1242 1 8 HELIX 10 AB1 LYS A 1242 ILE A 1258 1 17 HELIX 11 AB2 GLY A 1274 SER A 1278 5 5 HELIX 12 AB3 ASP A 1301 GLY A 1311 1 11 HELIX 13 AB4 LYS A 1312 GLY A 1325 1 14 SHEET 1 AA1 2 VAL A 904 PHE A 905 0 SHEET 2 AA1 2 ALA A 929 GLU A 930 -1 O GLU A 930 N VAL A 904 SHEET 1 AA2 4 ILE A 909 VAL A 914 0 SHEET 2 AA2 4 SER A 996 VAL A1005 1 O THR A1000 N TYR A 910 SHEET 3 AA2 4 ILE A 980 PHE A 988 -1 N ALA A 987 O SER A 997 SHEET 4 AA2 4 ARG A 943 ASP A 947 -1 N ARG A 945 O VAL A 986 SHEET 1 AA3 3 PRO A 923 THR A 926 0 SHEET 2 AA3 3 ARG A 966 THR A 969 -1 O VAL A 967 N THR A 925 SHEET 3 AA3 3 PHE A 958 VAL A 960 -1 N ASP A 959 O VAL A 968 SHEET 1 AA4 2 ARG A1013 PHE A1014 0 SHEET 2 AA4 2 ALA A1039 ALA A1040 -1 O ALA A1040 N ARG A1013 SHEET 1 AA5 3 GLU A1018 TYR A1019 0 SHEET 2 AA5 3 THR A1106 GLN A1114 1 O TYR A1110 N TYR A1019 SHEET 3 AA5 3 VAL A1024 SER A1025 1 N VAL A1024 O GLU A1112 SHEET 1 AA6 4 GLU A1018 TYR A1019 0 SHEET 2 AA6 4 THR A1106 GLN A1114 1 O TYR A1110 N TYR A1019 SHEET 3 AA6 4 SER A1081 SER A1090 -1 N LEU A1084 O VAL A1109 SHEET 4 AA6 4 ILE A1046 ALA A1052 -1 N ALA A1052 O ARG A1085 SHEET 1 AA7 3 VAL A1033 VAL A1036 0 SHEET 2 AA7 3 VAL A1067 VAL A1070 -1 O ILE A1068 N GLY A1035 SHEET 3 AA7 3 PHE A1059 ASN A1062 -1 N GLY A1060 O TYR A1069 SHEET 1 AA8 2 VAL A1122 PHE A1123 0 SHEET 2 AA8 2 ALA A1147 THR A1148 -1 O THR A1148 N VAL A1122 SHEET 1 AA9 4 PHE A1127 SER A1133 0 SHEET 2 AA9 4 SER A1212 VAL A1222 1 O LEU A1218 N GLY A1130 SHEET 3 AA9 4 TYR A1196 THR A1204 -1 N PHE A1199 O VAL A1217 SHEET 4 AA9 4 ALA A1159 ILE A1163 -1 N ARG A1161 O ILE A1202 SHEET 1 AB1 3 SER A1141 ARG A1144 0 SHEET 2 AB1 3 LEU A1182 THR A1185 -1 O ILE A1183 N LEU A1143 SHEET 3 AB1 3 PHE A1174 VAL A1176 -1 N VAL A1175 O LYS A1184 SHEET 1 AB2 4 LYS A1262 HIS A1273 0 SHEET 2 AB2 4 LEU A1279 ILE A1292 -1 O LEU A1279 N HIS A1273 SHEET 3 AB2 4 GLN A1228 SER A1232 -1 N GLN A1228 O VAL A1289 SHEET 4 AB2 4 ILE A1330 ARG A1334 -1 O ARG A1334 N VAL A1229 LINK OG SER A 996 C1 MAN A1405 1555 1555 1.45 LINK OG SER A 998 C1 MAN A1408 1555 1555 1.48 LINK OG1 THR A1000 C1 MAN A1406 1555 1555 1.45 LINK ND2 ASN A1063 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A1154 C1 NAG C 1 1555 1555 1.48 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.47 LINK OD1 ASN A 899 CA CA A1412 1555 1555 2.36 LINK O TYR A 901 CA CA A1412 1555 1555 2.25 LINK OD1 ASP A 931 CA CA A1412 1555 1555 2.39 LINK OD2 ASP A 931 CA CA A1412 1555 1555 2.71 LINK OD2 ASP A 933 CA CA A1412 1555 1555 2.36 LINK O ALA A 939 CA CA A1412 1555 1555 2.55 LINK OD1 ASP A 989 CA CA A1412 1555 1555 2.46 LINK OD2 ASP A 989 CA CA A1412 1555 1555 3.02 LINK OE2 GLU A1026 CA CA A1409 1555 1555 2.42 LINK OE1 GLU A1026 CA CA A1411 1555 1555 2.45 LINK OD1 ASP A1075 CA CA A1411 1555 1555 2.24 LINK OE1 GLU A1077 CA CA A1409 1555 1555 2.64 LINK OE2 GLU A1077 CA CA A1409 1555 1555 3.04 LINK OE2 GLU A1077 CA CA A1411 1555 1555 2.41 LINK OD1 ASP A1115 CA CA A1409 1555 1555 2.25 LINK O GLU A1116 CA CA A1409 1555 1555 2.39 LINK OD1 ASN A1117 CA CA A1410 1555 1555 2.28 LINK OD1 ASP A1118 CA CA A1409 1555 1555 2.65 LINK OD2 ASP A1118 CA CA A1411 1555 1555 2.19 LINK O HIS A1119 CA CA A1410 1555 1555 2.38 LINK OD1 ASP A1149 CA CA A1410 1555 1555 3.03 LINK OD1 ASP A1151 CA CA A1409 1555 1555 2.25 LINK OD2 ASP A1151 CA CA A1410 1555 1555 2.42 LINK O TYR A1155 CA CA A1410 1555 1555 2.54 LINK OD2 ASP A1205 CA CA A1410 1555 1555 2.55 CISPEP 1 GLU A 992 PRO A 993 0 -16.37 CRYST1 129.507 170.059 91.528 90.00 90.00 90.00 C 2 2 21 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 0.007722 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010926 0.00000