HEADER CELL ADHESION 26-JUN-19 6PIM TITLE CRYSTAL STRUCTURE OF HUMAN PROTOCADHERIN-1 EC3-4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTOCADHERIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CADHERIN-LIKE PROTEIN 1,PROTOCADHERIN-42,PC42; COMPND 5 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: PCDH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ADHESION, CALCIUM-BINDING, ASTHMA, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR D.MODAK,M.SOTOMAYOR REVDAT 3 11-OCT-23 6PIM 1 LINK REVDAT 2 16-OCT-19 6PIM 1 JRNL REVDAT 1 09-OCT-19 6PIM 0 JRNL AUTH D.MODAK,M.SOTOMAYOR JRNL TITL IDENTIFICATION OF AN ADHESIVE INTERFACE FOR THE JRNL TITL 2 NON-CLUSTERED DELTA 1 PROTOCADHERIN-1 INVOLVED IN JRNL TITL 3 RESPIRATORY DISEASES. JRNL REF COMMUN BIOL V. 2 354 2019 JRNL REFN ESSN 2399-3642 JRNL PMID 31583286 JRNL DOI 10.1038/S42003-019-0586-0 REMARK 2 REMARK 2 RESOLUTION. 3.05 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) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 6899 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 334 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) : 3.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 456 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 20 REMARK 3 BIN FREE R VALUE : 0.4650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1533 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31000 REMARK 3 B22 (A**2) : 1.31000 REMARK 3 B33 (A**2) : -2.63000 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): 0.997 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.392 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.301 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 36.760 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1551 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1439 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2106 ; 1.536 ; 1.652 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3348 ; 1.189 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 196 ; 9.645 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;32.954 ;23.295 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 262 ;18.141 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.032 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 214 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1746 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 290 ; 0.002 ; 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): 796 ; 1.955 ; 4.465 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 795 ; 1.943 ; 4.465 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 988 ; 3.209 ; 6.682 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 989 ; 3.209 ; 6.683 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 754 ; 2.154 ; 4.759 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 752 ; 2.150 ; 4.758 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1118 ; 3.551 ; 7.031 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5960 ; 6.481 ;84.892 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5958 ; 6.475 ;84.895 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 216 A 325 REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 RESIDUE RANGE : A 503 A 503 REMARK 3 RESIDUE RANGE : A 504 A 504 REMARK 3 ORIGIN FOR THE GROUP (A): -51.6511 4.0598 1.6630 REMARK 3 T TENSOR REMARK 3 T11: 0.0508 T22: 0.0995 REMARK 3 T33: 0.0474 T12: 0.0031 REMARK 3 T13: 0.0247 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 1.6423 L22: 7.2128 REMARK 3 L33: 2.5190 L12: -1.1540 REMARK 3 L13: -0.5658 L23: 1.8888 REMARK 3 S TENSOR REMARK 3 S11: 0.0745 S12: 0.1032 S13: 0.2435 REMARK 3 S21: 0.0145 S22: 0.0900 S23: -0.3217 REMARK 3 S31: -0.2697 S32: 0.2385 S33: -0.1645 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 326 A 438 REMARK 3 RESIDUE RANGE : A 502 A 502 REMARK 3 ORIGIN FOR THE GROUP (A): -36.8906 -38.2026 -10.8422 REMARK 3 T TENSOR REMARK 3 T11: 0.1133 T22: 0.2575 REMARK 3 T33: 0.0946 T12: 0.0832 REMARK 3 T13: 0.0586 T23: -0.0308 REMARK 3 L TENSOR REMARK 3 L11: 3.2572 L22: 6.1385 REMARK 3 L33: 5.2921 L12: -2.6202 REMARK 3 L13: -0.9697 L23: 4.0884 REMARK 3 S TENSOR REMARK 3 S11: -0.0017 S12: 0.1942 S13: -0.1274 REMARK 3 S21: -0.0992 S22: 0.2577 S23: -0.4325 REMARK 3 S31: 0.2121 S32: 0.0983 S33: -0.2560 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 6PIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000242622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-16 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 : 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) : 0.97921 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7363 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 1.02700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.670 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: 5DZV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 20% PEG 4000, 0.6 M REMARK 280 SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 62.78450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.78450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.64700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.78450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 62.78450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.64700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 62.78450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.78450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.64700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 62.78450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.78450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.64700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 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 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 MET A 214 REMARK 465 ASP A 215 REMARK 465 LEU A 337 REMARK 465 VAL A 338 REMARK 465 THR A 339 REMARK 465 HIS A 340 REMARK 465 GLN A 341 REMARK 465 ASP A 342 REMARK 465 GLY A 343 REMARK 465 MET A 344 REMARK 465 ALA A 345 REMARK 465 ASN A 346 REMARK 465 ILE A 347 REMARK 465 SER A 348 REMARK 465 GLU A 349 REMARK 465 THR A 391 REMARK 465 GLY A 392 REMARK 465 SER A 393 REMARK 465 ASP A 394 REMARK 465 SER A 395 REMARK 465 TYR A 409 REMARK 465 GLU A 410 REMARK 465 LYS A 411 REMARK 465 VAL A 412 REMARK 465 LYS A 413 REMARK 465 VAL A 439 REMARK 465 VAL A 440 REMARK 465 ASP A 441 REMARK 465 VAL A 442 REMARK 465 ASN A 443 REMARK 465 ASP A 444 REMARK 465 ASN A 445 REMARK 465 ALA A 446 REMARK 465 LEU A 447 REMARK 465 GLU A 448 REMARK 465 HIS A 449 REMARK 465 HIS A 450 REMARK 465 HIS A 451 REMARK 465 HIS A 452 REMARK 465 HIS A 453 REMARK 465 HIS A 454 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 304 -177.13 -69.26 REMARK 500 PRO A 382 24.18 -78.60 REMARK 500 GLN A 402 -168.26 -126.81 REMARK 500 LEU A 435 130.78 -177.15 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 A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 217 OD1 REMARK 620 2 ASN A 219 O 91.4 REMARK 620 3 ASP A 249 OD1 150.1 97.3 REMARK 620 4 ASP A 249 OD2 150.3 103.3 54.1 REMARK 620 5 ASP A 251 OD2 66.8 95.0 83.9 135.6 REMARK 620 6 ASN A 255 O 83.3 169.7 91.7 77.9 91.0 REMARK 620 7 ASP A 304 OD2 81.2 101.6 124.4 70.7 144.2 68.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 234 OE1 REMARK 620 2 GLU A 291 OE1 99.4 REMARK 620 3 GLU A 291 OE2 108.7 52.5 REMARK 620 4 ASP A 322 OD1 89.0 121.8 70.2 REMARK 620 5 MET A 323 O 84.9 148.3 154.8 89.4 REMARK 620 6 ASP A 325 OD1 90.7 77.1 127.6 160.9 71.5 REMARK 620 7 ASP A 366 OD1 157.2 85.8 92.1 107.2 79.5 68.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 234 OE2 REMARK 620 2 ASP A 289 OD1 83.2 REMARK 620 3 GLU A 291 OE1 85.1 105.3 REMARK 620 4 ASP A 325 OD2 81.3 153.5 94.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 324 OD1 REMARK 620 2 ASN A 326 O 101.1 REMARK 620 3 ASP A 364 OD1 144.0 103.2 REMARK 620 4 ASP A 364 OD2 164.8 72.3 50.8 REMARK 620 5 ASP A 366 OD2 80.9 77.1 79.1 110.1 REMARK 620 6 ASN A 370 O 91.5 165.3 62.2 97.1 97.9 REMARK 620 7 ASP A 423 OD1 101.3 107.6 96.2 68.9 174.1 76.7 REMARK 620 8 ASP A 423 OD2 62.4 94.9 139.9 104.0 140.3 97.6 43.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6BX7 RELATED DB: PDB REMARK 900 PCDH1 EC1-4 REMARK 900 RELATED ID: 6MGA RELATED DB: PDB REMARK 900 PCDH1 EC1-4 GLYCOSYLATED DBREF 6PIM A 215 446 UNP Q08174 PCDH1_HUMAN 272 503 SEQADV 6PIM MET A 214 UNP Q08174 INITIATING METHIONINE SEQADV 6PIM LEU A 447 UNP Q08174 EXPRESSION TAG SEQADV 6PIM GLU A 448 UNP Q08174 EXPRESSION TAG SEQADV 6PIM HIS A 449 UNP Q08174 EXPRESSION TAG SEQADV 6PIM HIS A 450 UNP Q08174 EXPRESSION TAG SEQADV 6PIM HIS A 451 UNP Q08174 EXPRESSION TAG SEQADV 6PIM HIS A 452 UNP Q08174 EXPRESSION TAG SEQADV 6PIM HIS A 453 UNP Q08174 EXPRESSION TAG SEQADV 6PIM HIS A 454 UNP Q08174 EXPRESSION TAG SEQRES 1 A 241 MET ASP THR ASN ASP ASN ALA PRO LYS PHE GLU ARG PRO SEQRES 2 A 241 SER TYR GLU ALA GLU LEU SER GLU ASN SER PRO ILE GLY SEQRES 3 A 241 HIS SER VAL ILE GLN VAL LYS ALA ASN ASP SER ASP GLN SEQRES 4 A 241 GLY ALA ASN ALA GLU ILE GLU TYR THR PHE HIS GLN ALA SEQRES 5 A 241 PRO GLU VAL VAL ARG ARG LEU LEU ARG LEU ASP ARG ASN SEQRES 6 A 241 THR GLY LEU ILE THR VAL GLN GLY PRO VAL ASP ARG GLU SEQRES 7 A 241 ASP LEU SER THR LEU ARG PHE SER VAL LEU ALA LYS ASP SEQRES 8 A 241 ARG GLY THR ASN PRO LYS SER ALA ARG ALA GLN VAL VAL SEQRES 9 A 241 VAL THR VAL LYS ASP MET ASN ASP ASN ALA PRO THR ILE SEQRES 10 A 241 GLU ILE ARG GLY ILE GLY LEU VAL THR HIS GLN ASP GLY SEQRES 11 A 241 MET ALA ASN ILE SER GLU ASP VAL ALA GLU GLU THR ALA SEQRES 12 A 241 VAL ALA LEU VAL GLN VAL SER ASP ARG ASP GLU GLY GLU SEQRES 13 A 241 ASN ALA ALA VAL THR CYS VAL VAL ALA GLY ASP VAL PRO SEQRES 14 A 241 PHE GLN LEU ARG GLN ALA SER GLU THR GLY SER ASP SER SEQRES 15 A 241 LYS LYS LYS TYR PHE LEU GLN THR THR THR PRO LEU ASP SEQRES 16 A 241 TYR GLU LYS VAL LYS ASP TYR THR ILE GLU ILE VAL ALA SEQRES 17 A 241 VAL ASP SER GLY ASN PRO PRO LEU SER SER THR ASN SER SEQRES 18 A 241 LEU LYS VAL GLN VAL VAL ASP VAL ASN ASP ASN ALA LEU SEQRES 19 A 241 GLU HIS HIS HIS HIS HIS HIS HET CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HETNAM CA CALCIUM ION FORMUL 2 CA 4(CA 2+) FORMUL 6 HOH *6(H2 O) HELIX 1 AA1 GLN A 252 GLU A 257 5 6 HELIX 2 AA2 PRO A 266 LEU A 272 1 7 HELIX 3 AA3 GLU A 367 ALA A 371 5 5 SHEET 1 AA1 2 LYS A 222 PHE A 223 0 SHEET 2 AA1 2 ALA A 247 ASN A 248 -1 O ASN A 248 N LYS A 222 SHEET 1 AA2 4 SER A 227 SER A 233 0 SHEET 2 AA2 4 SER A 311 LYS A 321 1 O THR A 319 N ALA A 230 SHEET 3 AA2 4 THR A 295 LYS A 303 -1 N ALA A 302 O ALA A 312 SHEET 4 AA2 4 GLU A 259 THR A 261 -1 N THR A 261 O LEU A 301 SHEET 1 AA3 3 SER A 241 GLN A 244 0 SHEET 2 AA3 3 LEU A 281 VAL A 284 -1 O ILE A 282 N ILE A 243 SHEET 3 AA3 3 LEU A 273 LEU A 275 -1 N ARG A 274 O THR A 283 SHEET 1 AA4 4 THR A 329 GLY A 334 0 SHEET 2 AA4 4 ALA A 358 SER A 363 -1 O LEU A 359 N ARG A 333 SHEET 3 AA4 4 LYS A 397 THR A 403 -1 O LEU A 401 N ALA A 358 SHEET 4 AA4 4 PHE A 383 GLN A 387 -1 N GLN A 384 O GLN A 402 SHEET 1 AA5 3 VAL A 373 ALA A 378 0 SHEET 2 AA5 3 GLU A 418 ASP A 423 -1 O VAL A 420 N VAL A 376 SHEET 3 AA5 3 SER A 430 ASN A 433 -1 O SER A 431 N ALA A 421 LINK OD1 ASN A 217 CA CA A 504 1555 1555 2.44 LINK O ASN A 219 CA CA A 504 1555 1555 2.53 LINK OE1 GLU A 234 CA CA A 501 1555 1555 2.19 LINK OE2 GLU A 234 CA CA A 503 1555 1555 2.46 LINK OD1 ASP A 249 CA CA A 504 1555 1555 2.46 LINK OD2 ASP A 249 CA CA A 504 1555 1555 2.40 LINK OD2 ASP A 251 CA CA A 504 1555 1555 2.74 LINK O ASN A 255 CA CA A 504 1555 1555 2.44 LINK OD1 ASP A 289 CA CA A 503 1555 1555 2.23 LINK OE1 GLU A 291 CA CA A 501 1555 1555 1.94 LINK OE2 GLU A 291 CA CA A 501 1555 1555 2.84 LINK OE1 GLU A 291 CA CA A 503 1555 1555 2.71 LINK OD2 ASP A 304 CA CA A 504 1555 1555 2.17 LINK OD1 ASP A 322 CA CA A 501 1555 1555 2.00 LINK O MET A 323 CA CA A 501 1555 1555 2.33 LINK OD1 ASN A 324 CA CA A 502 1555 1555 2.46 LINK OD1 ASP A 325 CA CA A 501 1555 1555 2.46 LINK OD2 ASP A 325 CA CA A 503 1555 1555 2.05 LINK O ASN A 326 CA CA A 502 1555 1555 2.29 LINK OD1 ASP A 364 CA CA A 502 1555 1555 2.74 LINK OD2 ASP A 364 CA CA A 502 1555 1555 2.21 LINK OD1 ASP A 366 CA CA A 501 1555 1555 2.30 LINK OD2 ASP A 366 CA CA A 502 1555 1555 2.45 LINK O ASN A 370 CA CA A 502 1555 1555 2.35 LINK OD1 ASP A 423 CA CA A 502 1555 1555 2.28 LINK OD2 ASP A 423 CA CA A 502 1555 1555 3.19 CISPEP 1 ASN A 426 PRO A 427 0 -10.25 SITE 1 AC1 6 GLU A 234 GLU A 291 ASP A 322 MET A 323 SITE 2 AC1 6 ASP A 325 ASP A 366 SITE 1 AC2 6 ASN A 324 ASN A 326 ASP A 364 ASP A 366 SITE 2 AC2 6 ASN A 370 ASP A 423 SITE 1 AC3 4 GLU A 234 ASP A 289 GLU A 291 ASP A 325 SITE 1 AC4 6 ASN A 217 ASN A 219 ASP A 249 ASP A 251 SITE 2 AC4 6 ASN A 255 ASP A 304 CRYST1 125.569 125.569 45.294 90.00 90.00 90.00 P 42 21 2 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 0.007964 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022078 0.00000