HEADER CELL ADHESION 04-MAY-15 4ZMW TITLE CRYSTAL STRUCTURE OF HUMAN P-CADHERIN (ENC-X-DIMER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CADHERIN-3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 108-320; COMPND 5 SYNONYM: PLACENTAL CADHERIN,P-CADHERIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDH3, CDHP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: CHAMPION PET SUMO KEYWDS DIMERIZATION, CONFORMATIONAL CHANGE, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,S.KUDO,K.TSUMOTO REVDAT 4 08-NOV-23 4ZMW 1 LINK REVDAT 3 19-FEB-20 4ZMW 1 JRNL REMARK REVDAT 2 21-SEP-16 4ZMW 1 JRNL REVDAT 1 07-SEP-16 4ZMW 0 JRNL AUTH S.KUDO,J.M.CAAVEIRO,K.TSUMOTO JRNL TITL ADHESIVE DIMERIZATION OF HUMAN P-CADHERIN CATALYZED BY A JRNL TITL 2 CHAPERONE-LIKE MECHANISM JRNL REF STRUCTURE V. 24 1523 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27545624 JRNL DOI 10.1016/J.STR.2016.07.002 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 31831 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1798 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2111 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3274 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.71000 REMARK 3 B22 (A**2) : -2.43000 REMARK 3 B33 (A**2) : 3.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.29000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.236 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.571 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3390 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3125 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4622 ; 1.592 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7252 ; 0.804 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 430 ; 7.007 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;37.326 ;25.762 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 549 ;15.766 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;10.384 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 536 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3789 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 691 ; 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): 1708 ; 2.569 ; 3.557 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1707 ; 2.568 ; 3.556 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2133 ; 4.062 ; 5.322 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2134 ; 4.061 ; 5.323 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1682 ; 3.278 ; 3.970 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1652 ; 2.805 ; 3.933 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2444 ; 4.471 ; 5.750 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3554 ; 6.799 ;27.894 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3522 ; 6.700 ;27.912 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4ZMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 1.000 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 : 33629 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 47.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 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: 4ZMN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.15 M LITHIUM SULFATE 7.5 MM NICKEL REMARK 280 SULFATE 100 MM TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.18450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.18450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 53.40500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -141.0 KCAL/MOL 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 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 MET B 0 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 TRP A 2 66.49 -101.01 REMARK 500 ASN A 12 48.70 38.74 REMARK 500 ALA A 43 -76.98 -102.48 REMARK 500 LYS A 156 46.93 -96.38 REMARK 500 ASP A 180 103.68 -173.34 REMARK 500 ALA B 43 -79.70 -106.52 REMARK 500 LYS B 156 31.06 -97.05 REMARK 500 HIS B 159 -169.88 -125.30 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 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 11 OE2 REMARK 620 2 GLU A 69 OE1 83.3 REMARK 620 3 GLU A 69 OE2 106.8 50.2 REMARK 620 4 ASP A 100 OD1 83.6 117.9 77.0 REMARK 620 5 GLN A 101 O 80.4 147.2 162.6 88.4 REMARK 620 6 ASP A 103 OD1 90.9 78.3 121.1 161.9 73.7 REMARK 620 7 ASP A 136 OD1 165.6 97.7 84.4 108.1 91.5 75.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 102 OD1 REMARK 620 2 HIS A 104 O 95.8 REMARK 620 3 ASP A 134 OD1 157.1 86.6 REMARK 620 4 ASP A 134 OD2 148.5 96.6 52.7 REMARK 620 5 ASP A 136 OD2 73.2 80.6 129.5 80.4 REMARK 620 6 ASN A 143 O 84.9 176.2 91.4 84.7 103.1 REMARK 620 7 ASP A 195 OD2 79.6 79.6 78.4 131.2 144.3 96.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 305 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 SO4 A 303 S 149.0 REMARK 620 3 SO4 A 303 O1 111.5 40.3 REMARK 620 4 SO4 A 303 O4 144.5 39.5 76.1 REMARK 620 5 SO4 A 304 S 82.6 122.0 125.1 122.6 REMARK 620 6 SO4 A 304 O3 93.0 98.5 90.3 122.1 34.9 REMARK 620 7 SO4 A 304 O4 73.6 137.3 159.2 112.0 34.2 69.1 REMARK 620 8 HOH A 403 O 83.2 100.6 120.2 64.4 114.0 148.6 80.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 11 OE2 REMARK 620 2 GLU B 69 OE1 86.1 REMARK 620 3 GLU B 69 OE2 113.4 48.8 REMARK 620 4 ASP B 100 OD1 85.0 118.9 81.1 REMARK 620 5 GLN B 101 O 85.3 151.1 157.0 87.7 REMARK 620 6 ASP B 103 OD1 90.5 78.3 116.8 161.7 74.2 REMARK 620 7 ASP B 136 OD1 160.9 96.3 81.6 110.0 83.5 71.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 102 OD1 REMARK 620 2 HIS B 104 O 97.8 REMARK 620 3 ASP B 134 OD1 151.0 95.4 REMARK 620 4 ASP B 134 OD2 151.0 96.8 50.6 REMARK 620 5 ASP B 136 OD2 77.6 76.5 130.8 81.8 REMARK 620 6 ASN B 143 O 82.0 177.5 85.9 82.3 101.0 REMARK 620 7 ASP B 195 OD2 76.9 81.2 79.8 130.2 143.2 101.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 308 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 104 NE2 REMARK 620 2 SO4 B 306 S 88.2 REMARK 620 3 SO4 B 306 O1 98.2 33.8 REMARK 620 4 SO4 B 306 O2 85.5 33.1 66.4 REMARK 620 5 SO4 B 307 S 129.8 132.7 104.4 144.7 REMARK 620 6 SO4 B 307 O1 93.9 169.5 135.8 157.4 40.5 REMARK 620 7 SO4 B 307 O3 165.6 106.2 94.2 106.2 38.7 72.0 REMARK 620 8 SO4 B 307 O4 117.0 109.5 76.2 139.0 33.8 60.4 59.2 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZML RELATED DB: PDB REMARK 900 RELATED ID: 4ZMN RELATED DB: PDB REMARK 900 RELATED ID: 4ZMO RELATED DB: PDB REMARK 900 RELATED ID: 4ZMP RELATED DB: PDB REMARK 900 RELATED ID: 4ZMQ RELATED DB: PDB REMARK 900 RELATED ID: 4ZMT RELATED DB: PDB REMARK 900 RELATED ID: 4ZMV RELATED DB: PDB REMARK 900 RELATED ID: 4ZMX RELATED DB: PDB REMARK 900 RELATED ID: 4ZMY RELATED DB: PDB REMARK 900 RELATED ID: 4ZMZ RELATED DB: PDB DBREF 4ZMW A 1 213 UNP P22223 CADH3_HUMAN 108 320 DBREF 4ZMW B 1 213 UNP P22223 CADH3_HUMAN 108 320 SEQADV 4ZMW MET A 0 UNP P22223 INITIATING METHIONINE SEQADV 4ZMW VAL A 22 UNP P22223 ASN 129 ENGINEERED MUTATION SEQADV 4ZMW MET B 0 UNP P22223 INITIATING METHIONINE SEQADV 4ZMW VAL B 22 UNP P22223 ASN 129 ENGINEERED MUTATION SEQRES 1 A 214 MET ASP TRP VAL VAL ALA PRO ILE SER VAL PRO GLU ASN SEQRES 2 A 214 GLY LYS GLY PRO PHE PRO GLN ARG LEU VAL GLN LEU LYS SEQRES 3 A 214 SER ASN LYS ASP ARG ASP THR LYS ILE PHE TYR SER ILE SEQRES 4 A 214 THR GLY PRO GLY ALA ASP SER PRO PRO GLU GLY VAL PHE SEQRES 5 A 214 ALA VAL GLU LYS GLU THR GLY TRP LEU LEU LEU ASN LYS SEQRES 6 A 214 PRO LEU ASP ARG GLU GLU ILE ALA LYS TYR GLU LEU PHE SEQRES 7 A 214 GLY HIS ALA VAL SER GLU ASN GLY ALA SER VAL GLU ASP SEQRES 8 A 214 PRO MET ASN ILE SER ILE ILE VAL THR ASP GLN ASN ASP SEQRES 9 A 214 HIS LYS PRO LYS PHE THR GLN ASP THR PHE ARG GLY SER SEQRES 10 A 214 VAL LEU GLU GLY VAL LEU PRO GLY THR SER VAL MET GLN SEQRES 11 A 214 VAL THR ALA THR ASP GLU ASP ASP ALA ILE TYR THR TYR SEQRES 12 A 214 ASN GLY VAL VAL ALA TYR SER ILE HIS SER GLN GLU PRO SEQRES 13 A 214 LYS ASP PRO HIS ASP LEU MET PHE THR ILE HIS ARG SER SEQRES 14 A 214 THR GLY THR ILE SER VAL ILE SER SER GLY LEU ASP ARG SEQRES 15 A 214 GLU LYS VAL PRO GLU TYR THR LEU THR ILE GLN ALA THR SEQRES 16 A 214 ASP MET ASP GLY ASP GLY SER THR THR THR ALA VAL ALA SEQRES 17 A 214 VAL VAL GLU ILE LEU ASP SEQRES 1 B 214 MET ASP TRP VAL VAL ALA PRO ILE SER VAL PRO GLU ASN SEQRES 2 B 214 GLY LYS GLY PRO PHE PRO GLN ARG LEU VAL GLN LEU LYS SEQRES 3 B 214 SER ASN LYS ASP ARG ASP THR LYS ILE PHE TYR SER ILE SEQRES 4 B 214 THR GLY PRO GLY ALA ASP SER PRO PRO GLU GLY VAL PHE SEQRES 5 B 214 ALA VAL GLU LYS GLU THR GLY TRP LEU LEU LEU ASN LYS SEQRES 6 B 214 PRO LEU ASP ARG GLU GLU ILE ALA LYS TYR GLU LEU PHE SEQRES 7 B 214 GLY HIS ALA VAL SER GLU ASN GLY ALA SER VAL GLU ASP SEQRES 8 B 214 PRO MET ASN ILE SER ILE ILE VAL THR ASP GLN ASN ASP SEQRES 9 B 214 HIS LYS PRO LYS PHE THR GLN ASP THR PHE ARG GLY SER SEQRES 10 B 214 VAL LEU GLU GLY VAL LEU PRO GLY THR SER VAL MET GLN SEQRES 11 B 214 VAL THR ALA THR ASP GLU ASP ASP ALA ILE TYR THR TYR SEQRES 12 B 214 ASN GLY VAL VAL ALA TYR SER ILE HIS SER GLN GLU PRO SEQRES 13 B 214 LYS ASP PRO HIS ASP LEU MET PHE THR ILE HIS ARG SER SEQRES 14 B 214 THR GLY THR ILE SER VAL ILE SER SER GLY LEU ASP ARG SEQRES 15 B 214 GLU LYS VAL PRO GLU TYR THR LEU THR ILE GLN ALA THR SEQRES 16 B 214 ASP MET ASP GLY ASP GLY SER THR THR THR ALA VAL ALA SEQRES 17 B 214 VAL VAL GLU ILE LEU ASP HET CA A 301 1 HET CA A 302 1 HET SO4 A 303 5 HET SO4 A 304 5 HET NI A 305 1 HET CA B 301 1 HET CA B 302 1 HET SO4 B 303 5 HET SO4 B 304 5 HET SO4 B 305 5 HET SO4 B 306 5 HET SO4 B 307 5 HET NI B 308 1 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION FORMUL 3 CA 4(CA 2+) FORMUL 5 SO4 7(O4 S 2-) FORMUL 7 NI 2(NI 2+) FORMUL 16 HOH *102(H2 O) HELIX 1 AA1 SER A 26 ASP A 31 5 6 HELIX 2 AA2 MET A 196 ASP A 199 5 4 HELIX 3 AA3 SER B 26 ASP B 31 5 6 HELIX 4 AA4 MET B 196 ASP B 199 5 4 SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA1 4 MET A 92 THR A 99 1 O ILE A 97 N ILE A 7 SHEET 3 AA1 4 LYS A 73 SER A 82 -1 N GLY A 78 O MET A 92 SHEET 4 AA1 4 ILE A 34 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 VAL A 22 SHEET 3 AA2 3 PHE A 51 VAL A 53 -1 N ALA A 52 O LEU A 61 SHEET 1 AA3 2 LYS A 107 PHE A 108 0 SHEET 2 AA3 2 ALA A 132 THR A 133 -1 O THR A 133 N LYS A 107 SHEET 1 AA4 4 THR A 112 LEU A 118 0 SHEET 2 AA4 4 THR A 202 LEU A 212 1 O LEU A 212 N VAL A 117 SHEET 3 AA4 4 GLU A 186 THR A 194 -1 N LEU A 189 O ALA A 207 SHEET 4 AA4 4 ALA A 147 GLU A 154 -1 N SER A 152 O THR A 190 SHEET 1 AA5 3 SER A 126 GLN A 129 0 SHEET 2 AA5 3 THR A 171 VAL A 174 -1 O ILE A 172 N MET A 128 SHEET 3 AA5 3 PHE A 163 ILE A 165 -1 N THR A 164 O SER A 173 SHEET 1 AA6 4 ILE B 7 PRO B 10 0 SHEET 2 AA6 4 MET B 92 THR B 99 1 O ILE B 97 N ILE B 7 SHEET 3 AA6 4 LYS B 73 SER B 82 -1 N LEU B 76 O ILE B 94 SHEET 4 AA6 4 ILE B 34 THR B 39 -1 N SER B 37 O HIS B 79 SHEET 1 AA7 3 GLN B 19 GLN B 23 0 SHEET 2 AA7 3 TRP B 59 LEU B 62 -1 O LEU B 60 N VAL B 22 SHEET 3 AA7 3 PHE B 51 VAL B 53 -1 N ALA B 52 O LEU B 61 SHEET 1 AA8 2 LYS B 107 PHE B 108 0 SHEET 2 AA8 2 ALA B 132 THR B 133 -1 O THR B 133 N LYS B 107 SHEET 1 AA9 4 THR B 112 LEU B 118 0 SHEET 2 AA9 4 THR B 202 LEU B 212 1 O GLU B 210 N GLY B 115 SHEET 3 AA9 4 GLU B 186 THR B 194 -1 N LEU B 189 O ALA B 207 SHEET 4 AA9 4 ALA B 147 GLU B 154 -1 N SER B 152 O THR B 190 SHEET 1 AB1 3 SER B 126 GLN B 129 0 SHEET 2 AB1 3 THR B 171 VAL B 174 -1 O ILE B 172 N VAL B 127 SHEET 3 AB1 3 PHE B 163 ILE B 165 -1 N THR B 164 O SER B 173 LINK OE2 GLU A 11 CA CA A 301 1555 1555 2.31 LINK OE1 GLU A 69 CA CA A 301 1555 1555 2.73 LINK OE2 GLU A 69 CA CA A 301 1555 1555 2.33 LINK OD1 ASP A 100 CA CA A 301 1555 1555 2.30 LINK O GLN A 101 CA CA A 301 1555 1555 2.39 LINK OD1 ASN A 102 CA CA A 302 1555 1555 2.23 LINK OD1 ASP A 103 CA CA A 301 1555 1555 2.32 LINK O HIS A 104 CA CA A 302 1555 1555 2.24 LINK NE2 HIS A 104 NI NI A 305 1555 1555 2.19 LINK OD1 ASP A 134 CA CA A 302 1555 1555 2.49 LINK OD2 ASP A 134 CA CA A 302 1555 1555 2.36 LINK OD1 ASP A 136 CA CA A 301 1555 1555 2.42 LINK OD2 ASP A 136 CA CA A 302 1555 1555 2.30 LINK O ASN A 143 CA CA A 302 1555 1555 2.36 LINK OD2 ASP A 195 CA CA A 302 1555 1555 2.22 LINK S SO4 A 303 NI NI A 305 1555 1555 2.30 LINK O1 SO4 A 303 NI NI A 305 1555 1555 1.87 LINK O4 SO4 A 303 NI NI A 305 1555 1555 2.02 LINK S SO4 A 304 NI NI A 305 1555 1555 2.63 LINK O3 SO4 A 304 NI NI A 305 1555 1555 2.43 LINK O4 SO4 A 304 NI NI A 305 1555 1555 1.85 LINK NI NI A 305 O HOH A 403 1555 1555 2.61 LINK OE2 GLU B 11 CA CA B 301 1555 1555 2.25 LINK OE1 GLU B 69 CA CA B 301 1555 1555 2.77 LINK OE2 GLU B 69 CA CA B 301 1555 1555 2.35 LINK OD1 ASP B 100 CA CA B 301 1555 1555 2.27 LINK O GLN B 101 CA CA B 301 1555 1555 2.43 LINK OD1 ASN B 102 CA CA B 302 1555 1555 2.22 LINK OD1 ASP B 103 CA CA B 301 1555 1555 2.31 LINK O HIS B 104 CA CA B 302 1555 1555 2.28 LINK NE2 HIS B 104 NI NI B 308 1555 1555 2.12 LINK OD1 ASP B 134 CA CA B 302 1555 1555 2.60 LINK OD2 ASP B 134 CA CA B 302 1555 1555 2.63 LINK OD1 ASP B 136 CA CA B 301 1555 1555 2.25 LINK OD2 ASP B 136 CA CA B 302 1555 1555 2.49 LINK O ASN B 143 CA CA B 302 1555 1555 2.29 LINK OD2 ASP B 195 CA CA B 302 1555 1555 2.33 LINK S SO4 B 306 NI NI B 308 1555 1555 2.66 LINK O1 SO4 B 306 NI NI B 308 1555 1555 2.49 LINK O2 SO4 B 306 NI NI B 308 1555 1555 1.87 LINK S SO4 B 307 NI NI B 308 1555 1555 2.27 LINK O1 SO4 B 307 NI NI B 308 1555 1555 1.98 LINK O3 SO4 B 307 NI NI B 308 1555 1555 2.22 LINK O4 SO4 B 307 NI NI B 308 1555 1555 2.65 CISPEP 1 GLY A 15 PRO A 16 0 11.58 CISPEP 2 PHE A 17 PRO A 18 0 5.20 CISPEP 3 PRO A 46 PRO A 47 0 -4.34 CISPEP 4 GLU A 154 PRO A 155 0 -5.36 CISPEP 5 ASP A 157 PRO A 158 0 6.72 CISPEP 6 GLY B 15 PRO B 16 0 10.91 CISPEP 7 PHE B 17 PRO B 18 0 3.88 CISPEP 8 PRO B 46 PRO B 47 0 -5.15 CISPEP 9 GLU B 154 PRO B 155 0 -15.02 CISPEP 10 ASP B 157 PRO B 158 0 6.29 SITE 1 AC1 6 GLU A 11 GLU A 69 ASP A 100 GLN A 101 SITE 2 AC1 6 ASP A 103 ASP A 136 SITE 1 AC2 6 ASN A 102 HIS A 104 ASP A 134 ASP A 136 SITE 2 AC2 6 ASN A 143 ASP A 195 SITE 1 AC3 6 ASP A 67 GLU A 69 HIS A 104 SO4 A 304 SITE 2 AC3 6 NI A 305 HOH A 403 SITE 1 AC4 6 ASP A 67 ASP A 103 HIS A 104 SO4 A 303 SITE 2 AC4 6 NI A 305 HOH A 403 SITE 1 AC5 4 HIS A 104 SO4 A 303 SO4 A 304 HOH A 403 SITE 1 AC6 6 GLU B 11 GLU B 69 ASP B 100 GLN B 101 SITE 2 AC6 6 ASP B 103 ASP B 136 SITE 1 AC7 6 ASN B 102 HIS B 104 ASP B 134 ASP B 136 SITE 2 AC7 6 ASN B 143 ASP B 195 SITE 1 AC8 7 ARG A 68 GLU A 135 HOH A 401 GLN B 110 SITE 2 AC8 7 PHE B 113 ARG B 114 HOH B 427 SITE 1 AC9 2 ARG A 181 ARG B 20 SITE 1 AD1 4 THR B 32 SER B 82 ASN B 84 ALA B 86 SITE 1 AD2 5 ASP B 67 ASP B 103 HIS B 104 SO4 B 307 SITE 2 AD2 5 NI B 308 SITE 1 AD3 5 ASP B 67 HIS B 104 GLU B 135 SO4 B 306 SITE 2 AD3 5 NI B 308 SITE 1 AD4 3 HIS B 104 SO4 B 306 SO4 B 307 CRYST1 94.369 106.810 77.579 90.00 94.86 90.00 C 1 2 1 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 0.010597 0.000000 0.000901 0.00000 SCALE2 0.000000 0.009362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012937 0.00000