HEADER CELL ADHESION/IMMUNE SYSTEM 14-MAY-16 5JYL TITLE HUMAN P-CADHERIN MEC1 WITH SCFV TSP7 BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: CADHERIN-3; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 108-207; COMPND 5 SYNONYM: PLACENTAL CADHERIN,P-CADHERIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SCFV TSP7; COMPND 9 CHAIN: B, D; 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: CDH3; 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_VARIANT: ROSETTA2; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PRA2 KEYWDS CADHERIN CELL ADHESION ANTIBODY PROTEIN-PROTEIN INTERACTION, KEYWDS 2 OXIDOREDUCTASE, CELL ADHESION-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,S.KUDO,K.TSUMOTO REVDAT 4 08-NOV-23 5JYL 1 REMARK REVDAT 3 19-FEB-20 5JYL 1 REMARK REVDAT 2 18-JAN-17 5JYL 1 JRNL REVDAT 1 28-DEC-16 5JYL 0 JRNL AUTH S.KUDO,J.M.M.CAAVEIRO,S.NAGATOISHI,T.MIYAFUSA,T.MATSUURA, JRNL AUTH 2 Y.SUDOU,K.TSUMOTO JRNL TITL DISRUPTION OF CELL ADHESION BY AN ANTIBODY TARGETING THE JRNL TITL 2 CELL-ADHESIVE INTERMEDIATE (X-DIMER) OF HUMAN P-CADHERIN JRNL REF SCI REP V. 7 39518 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28045038 JRNL DOI 10.1038/SREP39518 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 109.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 22077 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1222 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1548 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4998 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75000 REMARK 3 B22 (A**2) : -1.10000 REMARK 3 B33 (A**2) : -0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.973 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.339 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.273 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.018 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5128 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4684 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6943 ; 1.291 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10844 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 640 ; 6.637 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;34.130 ;24.732 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 848 ;15.941 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.241 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 755 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5799 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1157 ; 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): 2575 ; 0.992 ; 2.546 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2574 ; 0.992 ; 2.546 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3207 ; 1.729 ; 3.812 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3208 ; 1.729 ; 3.813 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2553 ; 1.046 ; 2.656 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2549 ; 1.028 ; 2.646 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3730 ; 1.776 ; 3.918 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5356 ; 3.507 ;19.579 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5348 ; 3.393 ;19.564 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 5 99 C 5 99 4972 0.13 0.05 REMARK 3 2 B 1 242 D 1 242 11223 0.16 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 100 REMARK 3 ORIGIN FOR THE GROUP (A): -20.3766 -4.3216 -40.4772 REMARK 3 T TENSOR REMARK 3 T11: 0.0751 T22: 0.0073 REMARK 3 T33: 0.0642 T12: 0.0100 REMARK 3 T13: 0.0627 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 4.8431 L22: 2.5937 REMARK 3 L33: 2.3321 L12: 0.7136 REMARK 3 L13: -0.2588 L23: 0.2476 REMARK 3 S TENSOR REMARK 3 S11: -0.1926 S12: -0.1293 S13: -0.1497 REMARK 3 S21: 0.1288 S22: 0.0746 S23: 0.0936 REMARK 3 S31: 0.2784 S32: -0.0051 S33: 0.1180 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 244 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2896 12.5556 -39.6528 REMARK 3 T TENSOR REMARK 3 T11: 0.0902 T22: 0.0243 REMARK 3 T33: 0.0486 T12: 0.0136 REMARK 3 T13: 0.0399 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.8150 L22: 2.2247 REMARK 3 L33: 2.2233 L12: -0.0074 REMARK 3 L13: -0.0913 L23: 0.8228 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: -0.0597 S13: 0.1419 REMARK 3 S21: 0.1379 S22: 0.0291 S23: 0.0251 REMARK 3 S31: -0.2529 S32: 0.0511 S33: -0.0217 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 5 C 100 REMARK 3 ORIGIN FOR THE GROUP (A): -25.2339 15.8939 -34.1594 REMARK 3 T TENSOR REMARK 3 T11: 0.0951 T22: 0.0303 REMARK 3 T33: 0.1310 T12: 0.0227 REMARK 3 T13: 0.0533 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 2.0503 L22: 2.9285 REMARK 3 L33: 4.8996 L12: 0.2033 REMARK 3 L13: -0.4547 L23: -0.9424 REMARK 3 S TENSOR REMARK 3 S11: -0.0047 S12: 0.0345 S13: 0.1330 REMARK 3 S21: -0.0357 S22: 0.0840 S23: 0.0599 REMARK 3 S31: -0.2852 S32: -0.0209 S33: -0.0794 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 242 REMARK 3 ORIGIN FOR THE GROUP (A): -20.0518 -3.6954 -6.6590 REMARK 3 T TENSOR REMARK 3 T11: 0.2654 T22: 0.2084 REMARK 3 T33: 0.1601 T12: 0.0754 REMARK 3 T13: 0.1262 T23: 0.0618 REMARK 3 L TENSOR REMARK 3 L11: 0.9493 L22: 1.7835 REMARK 3 L33: 3.4437 L12: -0.0895 REMARK 3 L13: 0.0432 L23: 0.4883 REMARK 3 S TENSOR REMARK 3 S11: 0.0162 S12: -0.0338 S13: -0.1589 REMARK 3 S21: 0.1039 S22: -0.0425 S23: -0.2471 REMARK 3 S31: 0.4967 S32: 0.4420 S33: 0.0263 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 5JYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23310 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 109.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1QOK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.70500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 0 REMARK 465 ASP A 1 REMARK 465 TRP A 2 REMARK 465 VAL A 3 REMARK 465 SER B 119 REMARK 465 SER B 120 REMARK 465 ALA B 121 REMARK 465 GLY B 122 REMARK 465 GLY B 123 REMARK 465 GLY B 124 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 GLY B 127 REMARK 465 GLY B 128 REMARK 465 GLY B 129 REMARK 465 GLY B 130 REMARK 465 SER B 131 REMARK 465 GLY B 132 REMARK 465 LYS B 245 REMARK 465 SER B 246 REMARK 465 ALA B 247 REMARK 465 HIS B 248 REMARK 465 HIS B 249 REMARK 465 HIS B 250 REMARK 465 HIS B 251 REMARK 465 HIS B 252 REMARK 465 HIS B 253 REMARK 465 MET C 0 REMARK 465 ASP C 1 REMARK 465 TRP C 2 REMARK 465 VAL C 3 REMARK 465 VAL C 4 REMARK 465 GLY D 42 REMARK 465 SER D 119 REMARK 465 SER D 120 REMARK 465 ALA D 121 REMARK 465 GLY D 122 REMARK 465 GLY D 123 REMARK 465 GLY D 124 REMARK 465 GLY D 125 REMARK 465 SER D 126 REMARK 465 GLY D 127 REMARK 465 GLY D 128 REMARK 465 GLY D 129 REMARK 465 GLY D 130 REMARK 465 SER D 131 REMARK 465 GLY D 132 REMARK 465 GLY D 133 REMARK 465 GLY D 134 REMARK 465 GLY D 135 REMARK 465 SER D 136 REMARK 465 ASP D 137 REMARK 465 GLU D 243 REMARK 465 ILE D 244 REMARK 465 LYS D 245 REMARK 465 SER D 246 REMARK 465 ALA D 247 REMARK 465 HIS D 248 REMARK 465 HIS D 249 REMARK 465 HIS D 250 REMARK 465 HIS D 251 REMARK 465 HIS D 252 REMARK 465 HIS D 253 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 22 147.32 -172.33 REMARK 500 ALA A 43 -73.78 -118.35 REMARK 500 ASN B 169 -2.80 67.81 REMARK 500 THR B 189 -51.57 75.49 REMARK 500 ASN B 215 72.96 42.84 REMARK 500 ASN C 22 146.90 -171.90 REMARK 500 ALA C 43 -73.87 -118.01 REMARK 500 ASN D 169 -2.95 68.55 REMARK 500 ASP D 179 -43.99 155.02 REMARK 500 THR D 189 -51.46 74.80 REMARK 500 ASN D 215 73.32 41.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JYM RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 MET 0 IN CHAIN A, C IS N-TERMINAL EXTENSION TO INHIBIT STRAND-SWAP REMARK 999 DIMERIZATION. ABOUT SCFV TSP7 (CHAIN B, D), RESIDUES 120- REMARK 999 138(SAGGGGSGGGGSGGGGSDI) BELONG TO THE LINKER JOINING THE HEAVY TO REMARK 999 THE LIGHT CHAIN OF THE ANTIBODY, AND RESIDUES 246-253(SAHHHHHH) REMARK 999 BELONG TO THE PURIFICATION TAG. DBREF 5JYL A 1 100 UNP P22223 CADH3_HUMAN 108 207 DBREF 5JYL B 1 253 PDB 5JYL 5JYL 1 253 DBREF 5JYL C 1 100 UNP P22223 CADH3_HUMAN 108 207 DBREF 5JYL D 1 253 PDB 5JYL 5JYL 1 253 SEQADV 5JYL MET A 0 UNP P22223 SEE SEQUENCE DETAILS SEQADV 5JYL MET C 0 UNP P22223 SEE SEQUENCE DETAILS SEQRES 1 A 101 MET ASP TRP VAL VAL ALA PRO ILE SER VAL PRO GLU ASN SEQRES 2 A 101 GLY LYS GLY PRO PHE PRO GLN ARG LEU ASN GLN LEU LYS SEQRES 3 A 101 SER ASN LYS ASP ARG ASP THR LYS ILE PHE TYR SER ILE SEQRES 4 A 101 THR GLY PRO GLY ALA ASP SER PRO PRO GLU GLY VAL PHE SEQRES 5 A 101 ALA VAL GLU LYS GLU THR GLY TRP LEU LEU LEU ASN LYS SEQRES 6 A 101 PRO LEU ASP ARG GLU GLU ILE ALA LYS TYR GLU LEU PHE SEQRES 7 A 101 GLY HIS ALA VAL SER GLU ASN GLY ALA SER VAL GLU ASP SEQRES 8 A 101 PRO MET ASN ILE SER ILE ILE VAL THR ASP SEQRES 1 B 253 GLN VAL GLN LEU GLN GLU SER GLY PRO GLU LEU VAL LYS SEQRES 2 B 253 PRO GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 B 253 TYR SER PHE THR ALA TYR ASN MET HIS TRP VAL LYS GLN SEQRES 4 B 253 SER HIS GLY LYS SER LEU GLU TRP ILE GLY PHE ILE ASP SEQRES 5 B 253 PRO TYR SER GLY ILE ILE THR TYR ASN GLN THR PHE LYS SEQRES 6 B 253 GLY LYS ALA THR LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 B 253 ALA TYR MET GLN LEU ASN SER LEU THR SER GLU ASP SER SEQRES 8 B 253 ALA VAL TYR TYR CYS ALA ARG ARG GLY TYR TYR ASP GLY SEQRES 9 B 253 GLY PHE ASP TYR TRP GLY GLN GLY THR THR LEU THR VAL SEQRES 10 B 253 SER SER SER ALA GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 11 B 253 SER GLY GLY GLY GLY SER ASP ILE ASP ILE GLN MET THR SEQRES 12 B 253 GLN THR THR SER SER LEU SER ALA SER LEU GLY ASP ARG SEQRES 13 B 253 VAL THR ILE SER CYS ARG ALA SER GLN ASP ILE THR ASN SEQRES 14 B 253 TYR LEU ASN TRP TYR GLN GLN LYS PRO ASP GLY THR VAL SEQRES 15 B 253 LYS LEU LEU ILE TYR TYR THR SER ARG LEU HIS SER GLY SEQRES 16 B 253 VAL PRO SER ARG PHE SER GLY SER GLY SER GLY THR ASP SEQRES 17 B 253 TYR SER LEU THR ILE SER ASN LEU GLU GLN GLU ASP ILE SEQRES 18 B 253 ALA THR TYR PHE CYS GLN GLN ASP SER LYS HIS PRO ARG SEQRES 19 B 253 THR PHE GLY GLY GLY THR LYS LEU GLU ILE LYS SER ALA SEQRES 20 B 253 HIS HIS HIS HIS HIS HIS SEQRES 1 C 101 MET ASP TRP VAL VAL ALA PRO ILE SER VAL PRO GLU ASN SEQRES 2 C 101 GLY LYS GLY PRO PHE PRO GLN ARG LEU ASN GLN LEU LYS SEQRES 3 C 101 SER ASN LYS ASP ARG ASP THR LYS ILE PHE TYR SER ILE SEQRES 4 C 101 THR GLY PRO GLY ALA ASP SER PRO PRO GLU GLY VAL PHE SEQRES 5 C 101 ALA VAL GLU LYS GLU THR GLY TRP LEU LEU LEU ASN LYS SEQRES 6 C 101 PRO LEU ASP ARG GLU GLU ILE ALA LYS TYR GLU LEU PHE SEQRES 7 C 101 GLY HIS ALA VAL SER GLU ASN GLY ALA SER VAL GLU ASP SEQRES 8 C 101 PRO MET ASN ILE SER ILE ILE VAL THR ASP SEQRES 1 D 253 GLN VAL GLN LEU GLN GLU SER GLY PRO GLU LEU VAL LYS SEQRES 2 D 253 PRO GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 D 253 TYR SER PHE THR ALA TYR ASN MET HIS TRP VAL LYS GLN SEQRES 4 D 253 SER HIS GLY LYS SER LEU GLU TRP ILE GLY PHE ILE ASP SEQRES 5 D 253 PRO TYR SER GLY ILE ILE THR TYR ASN GLN THR PHE LYS SEQRES 6 D 253 GLY LYS ALA THR LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 D 253 ALA TYR MET GLN LEU ASN SER LEU THR SER GLU ASP SER SEQRES 8 D 253 ALA VAL TYR TYR CYS ALA ARG ARG GLY TYR TYR ASP GLY SEQRES 9 D 253 GLY PHE ASP TYR TRP GLY GLN GLY THR THR LEU THR VAL SEQRES 10 D 253 SER SER SER ALA GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 11 D 253 SER GLY GLY GLY GLY SER ASP ILE ASP ILE GLN MET THR SEQRES 12 D 253 GLN THR THR SER SER LEU SER ALA SER LEU GLY ASP ARG SEQRES 13 D 253 VAL THR ILE SER CYS ARG ALA SER GLN ASP ILE THR ASN SEQRES 14 D 253 TYR LEU ASN TRP TYR GLN GLN LYS PRO ASP GLY THR VAL SEQRES 15 D 253 LYS LEU LEU ILE TYR TYR THR SER ARG LEU HIS SER GLY SEQRES 16 D 253 VAL PRO SER ARG PHE SER GLY SER GLY SER GLY THR ASP SEQRES 17 D 253 TYR SER LEU THR ILE SER ASN LEU GLU GLN GLU ASP ILE SEQRES 18 D 253 ALA THR TYR PHE CYS GLN GLN ASP SER LYS HIS PRO ARG SEQRES 19 D 253 THR PHE GLY GLY GLY THR LYS LEU GLU ILE LYS SER ALA SEQRES 20 D 253 HIS HIS HIS HIS HIS HIS HET GOL B 301 6 HET PO4 B 302 5 HET CL B 303 1 HET CL D 301 1 HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 PO4 O4 P 3- FORMUL 7 CL 2(CL 1-) FORMUL 9 HOH *84(H2 O) HELIX 1 AA1 SER B 28 TYR B 32 5 5 HELIX 2 AA2 GLN B 62 LYS B 65 5 4 HELIX 3 AA3 LYS B 74 SER B 76 5 3 HELIX 4 AA4 THR B 87 SER B 91 5 5 HELIX 5 AA5 GLU B 217 ILE B 221 5 5 HELIX 6 AA6 SER D 28 TYR D 32 5 5 HELIX 7 AA7 GLN D 62 LYS D 65 5 4 HELIX 8 AA8 LYS D 74 SER D 76 5 3 HELIX 9 AA9 THR D 87 SER D 91 5 5 HELIX 10 AB1 GLU D 217 ILE D 221 5 5 SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA1 4 MET A 92 THR A 99 1 O SER A 95 N ILE A 7 SHEET 3 AA1 4 LYS A 73 VAL A 81 -1 N LEU A 76 O ILE A 94 SHEET 4 AA1 4 PHE A 35 THR A 39 -1 N PHE A 35 O VAL A 81 SHEET 1 AA2 3 GLN A 19 GLN A 23 0 SHEET 2 AA2 3 TRP A 59 LEU A 62 -1 O LEU A 60 N ASN A 22 SHEET 3 AA2 3 PHE A 51 VAL A 53 -1 N ALA A 52 O LEU A 61 SHEET 1 AA3 4 GLN B 3 GLU B 6 0 SHEET 2 AA3 4 VAL B 18 SER B 25 -1 O LYS B 23 N GLN B 5 SHEET 3 AA3 4 THR B 78 LEU B 83 -1 O MET B 81 N MET B 20 SHEET 4 AA3 4 ALA B 68 ASP B 73 -1 N THR B 71 O TYR B 80 SHEET 1 AA4 6 GLU B 10 VAL B 12 0 SHEET 2 AA4 6 THR B 113 VAL B 117 1 O THR B 114 N GLU B 10 SHEET 3 AA4 6 ALA B 92 ARG B 99 -1 N ALA B 92 O LEU B 115 SHEET 4 AA4 6 MET B 34 SER B 40 -1 N VAL B 37 O TYR B 95 SHEET 5 AA4 6 SER B 44 ILE B 51 -1 O GLU B 46 N LYS B 38 SHEET 6 AA4 6 ILE B 58 TYR B 60 -1 O THR B 59 N PHE B 50 SHEET 1 AA5 4 GLU B 10 VAL B 12 0 SHEET 2 AA5 4 THR B 113 VAL B 117 1 O THR B 114 N GLU B 10 SHEET 3 AA5 4 ALA B 92 ARG B 99 -1 N ALA B 92 O LEU B 115 SHEET 4 AA5 4 PHE B 106 TRP B 109 -1 O TYR B 108 N ARG B 98 SHEET 1 AA6 4 MET B 142 THR B 143 0 SHEET 2 AA6 4 VAL B 157 ALA B 163 -1 O ARG B 162 N THR B 143 SHEET 3 AA6 4 ASP B 208 ILE B 213 -1 O LEU B 211 N ILE B 159 SHEET 4 AA6 4 PHE B 200 SER B 205 -1 N SER B 201 O THR B 212 SHEET 1 AA7 6 SER B 148 SER B 150 0 SHEET 2 AA7 6 THR B 240 GLU B 243 1 O LYS B 241 N LEU B 149 SHEET 3 AA7 6 ALA B 222 GLN B 228 -1 N TYR B 224 O THR B 240 SHEET 4 AA7 6 LEU B 171 GLN B 176 -1 N TYR B 174 O PHE B 225 SHEET 5 AA7 6 VAL B 182 TYR B 187 -1 O ILE B 186 N TRP B 173 SHEET 6 AA7 6 ARG B 191 LEU B 192 -1 O ARG B 191 N TYR B 187 SHEET 1 AA8 4 SER B 148 SER B 150 0 SHEET 2 AA8 4 THR B 240 GLU B 243 1 O LYS B 241 N LEU B 149 SHEET 3 AA8 4 ALA B 222 GLN B 228 -1 N TYR B 224 O THR B 240 SHEET 4 AA8 4 THR B 235 PHE B 236 -1 O THR B 235 N GLN B 228 SHEET 1 AA9 4 ILE C 7 PRO C 10 0 SHEET 2 AA9 4 MET C 92 THR C 99 1 O SER C 95 N ILE C 7 SHEET 3 AA9 4 LYS C 73 VAL C 81 -1 N LEU C 76 O ILE C 94 SHEET 4 AA9 4 PHE C 35 THR C 39 -1 N PHE C 35 O VAL C 81 SHEET 1 AB1 3 GLN C 19 GLN C 23 0 SHEET 2 AB1 3 TRP C 59 LEU C 62 -1 O LEU C 60 N ASN C 22 SHEET 3 AB1 3 PHE C 51 VAL C 53 -1 N ALA C 52 O LEU C 61 SHEET 1 AB2 4 GLN D 3 GLU D 6 0 SHEET 2 AB2 4 VAL D 18 SER D 25 -1 O LYS D 23 N GLN D 5 SHEET 3 AB2 4 THR D 78 LEU D 83 -1 O LEU D 83 N VAL D 18 SHEET 4 AB2 4 ALA D 68 ASP D 73 -1 N ASP D 73 O THR D 78 SHEET 1 AB3 6 GLU D 10 VAL D 12 0 SHEET 2 AB3 6 THR D 113 VAL D 117 1 O THR D 114 N GLU D 10 SHEET 3 AB3 6 ALA D 92 ARG D 99 -1 N ALA D 92 O LEU D 115 SHEET 4 AB3 6 MET D 34 GLN D 39 -1 N VAL D 37 O TYR D 95 SHEET 5 AB3 6 LEU D 45 ILE D 51 -1 O GLU D 46 N LYS D 38 SHEET 6 AB3 6 ILE D 58 TYR D 60 -1 O THR D 59 N PHE D 50 SHEET 1 AB4 4 GLU D 10 VAL D 12 0 SHEET 2 AB4 4 THR D 113 VAL D 117 1 O THR D 114 N GLU D 10 SHEET 3 AB4 4 ALA D 92 ARG D 99 -1 N ALA D 92 O LEU D 115 SHEET 4 AB4 4 PHE D 106 TRP D 109 -1 O TYR D 108 N ARG D 98 SHEET 1 AB5 4 MET D 142 THR D 143 0 SHEET 2 AB5 4 VAL D 157 ALA D 163 -1 O ARG D 162 N THR D 143 SHEET 3 AB5 4 ASP D 208 ILE D 213 -1 O LEU D 211 N ILE D 159 SHEET 4 AB5 4 PHE D 200 SER D 205 -1 N SER D 201 O THR D 212 SHEET 1 AB6 5 ARG D 191 LEU D 192 0 SHEET 2 AB6 5 VAL D 182 TYR D 187 -1 N TYR D 187 O ARG D 191 SHEET 3 AB6 5 LEU D 171 GLN D 176 -1 N TRP D 173 O ILE D 186 SHEET 4 AB6 5 ALA D 222 GLN D 228 -1 O PHE D 225 N TYR D 174 SHEET 5 AB6 5 THR D 235 PHE D 236 -1 O THR D 235 N GLN D 228 SHEET 1 AB7 5 ARG D 191 LEU D 192 0 SHEET 2 AB7 5 VAL D 182 TYR D 187 -1 N TYR D 187 O ARG D 191 SHEET 3 AB7 5 LEU D 171 GLN D 176 -1 N TRP D 173 O ILE D 186 SHEET 4 AB7 5 ALA D 222 GLN D 228 -1 O PHE D 225 N TYR D 174 SHEET 5 AB7 5 THR D 240 LEU D 242 -1 O THR D 240 N TYR D 224 SSBOND 1 CYS B 22 CYS B 96 1555 1555 1.98 SSBOND 2 CYS B 161 CYS B 226 1555 1555 2.04 SSBOND 3 CYS D 22 CYS D 96 1555 1555 2.00 SSBOND 4 CYS D 161 CYS D 226 1555 1555 2.04 CISPEP 1 GLY A 15 PRO A 16 0 7.42 CISPEP 2 PHE A 17 PRO A 18 0 7.05 CISPEP 3 PRO A 46 PRO A 47 0 -4.25 CISPEP 4 THR A 99 ASP A 100 0 17.23 CISPEP 5 HIS B 41 GLY B 42 0 6.44 CISPEP 6 HIS B 232 PRO B 233 0 -1.36 CISPEP 7 GLY C 15 PRO C 16 0 4.65 CISPEP 8 PHE C 17 PRO C 18 0 5.19 CISPEP 9 PRO C 46 PRO C 47 0 -2.06 CISPEP 10 HIS D 232 PRO D 233 0 -3.37 SITE 1 AC1 3 THR B 30 TYR B 54 LYS B 74 SITE 1 AC2 4 GLN B 111 GLY B 112 THR B 114 HOH B 422 SITE 1 AC3 2 TYR B 108 HIS B 193 SITE 1 AC4 1 TYR D 108 CRYST1 66.570 49.410 111.660 90.00 101.89 90.00 P 1 21 1 4 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 0.015022 0.000000 0.003163 0.00000 SCALE2 0.000000 0.020239 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009152 0.00000