HEADER CELL ADHESION 16-SEP-05 2B1O TITLE SOLUTION STRUCTURE OF CA2+-BOUND DDCAD-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALCIUM-DEPENDENT CELL ADHESION MOLECULE-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CA2+-BOUND DDCAD-1, DDCAD-1, GP24; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_TAXID: 44689; SOURCE 4 GENE: CADA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-M KEYWDS DDCAD-1, CALCIUM, CELL ADHERISON, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.LIN,S.SRISKANTHADEVAN,H.B.HUANG,C.H.SIU,D.W.YANG REVDAT 5 09-MAR-22 2B1O 1 REMARK LINK REVDAT 4 24-FEB-09 2B1O 1 VERSN REVDAT 3 01-JAN-08 2B1O 1 JRNL REVDAT 2 24-OCT-06 2B1O 1 JRNL REMARK REVDAT 1 26-SEP-06 2B1O 0 JRNL AUTH Z.LIN,S.SRISKANTHADEVAN,H.B.HUANG,C.H.SIU,D.W.YANG JRNL TITL SOLUTION STRUCTURES OF THE ADHESION MOLECULE DDCAD-1 REVEAL JRNL TITL 2 NEW INSIGHTS INTO CA(2+)-DEPENDENT CELL-CELL ADHESION JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 1016 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 17057715 JRNL DOI 10.1038/NSMB1162 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.LIN,H.B.HUANG,C.H.SIU,D.W.YANG REMARK 1 TITL (1)H, (13)C AND (15)N RESONANCE ASSIGNMENTS OF CA(2+)-FREE REMARK 1 TITL 2 DDCAD-1: A CA(2+)-DEPENDENT CELL-CELL ADHESION MOLECULE REMARK 1 REF J.BIOMOL.NMR V. 30 375 2004 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 15756470 REMARK 1 DOI 10.1007/S10858-005-2336-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2004.126.16.02, AMBER 7.0 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), DAVID (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ENERGY MINIMIZATION IN AMBER FORCE REMARK 3 FIELD REMARK 4 REMARK 4 2B1O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034564. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 5MM CACL2, 0.05MM SODIUM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5MM DDCAD-1 U-15N, 13C; 5MM REMARK 210 CACL2, 10MM PIPES BUFFER, 2MM REMARK 210 DTT, 0.05MM SODIUM AZIDE, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C/15N-SEPARATED_NOESY; REMARK 210 3D_15N-SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.2.2.01, CYANA 1.0.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 GLU A 59 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 10 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 PHE A 12 45.23 -79.94 REMARK 500 1 CYS A 16 72.33 63.98 REMARK 500 1 ASN A 33 54.75 -144.44 REMARK 500 1 ASP A 35 86.31 63.39 REMARK 500 1 LYS A 36 -79.28 -174.92 REMARK 500 1 ASP A 39 -75.23 -39.44 REMARK 500 1 LYS A 40 42.25 37.80 REMARK 500 1 MET A 42 -45.45 -152.91 REMARK 500 1 HIS A 57 35.96 -143.81 REMARK 500 1 ILE A 60 38.82 -93.21 REMARK 500 1 PRO A 63 7.34 -69.25 REMARK 500 1 GLU A 70 79.92 -113.60 REMARK 500 1 LEU A 71 102.66 -46.52 REMARK 500 1 GLN A 73 109.53 -55.50 REMARK 500 1 LEU A 86 43.05 -161.73 REMARK 500 1 VAL A 108 -48.91 -138.46 REMARK 500 1 SER A 110 53.34 -68.53 REMARK 500 1 THR A 111 -45.01 -137.53 REMARK 500 1 ALA A 112 158.51 56.94 REMARK 500 1 TYR A 122 93.61 -26.08 REMARK 500 1 ASP A 125 94.53 -54.25 REMARK 500 1 ASP A 131 103.81 -49.20 REMARK 500 1 PRO A 141 -175.26 -69.25 REMARK 500 1 TYR A 165 107.28 -58.16 REMARK 500 1 THR A 179 27.65 -145.32 REMARK 500 1 THR A 190 -50.86 -132.51 REMARK 500 1 SER A 211 109.91 -168.04 REMARK 500 2 PHE A 12 44.79 -101.86 REMARK 500 2 CYS A 16 64.46 61.85 REMARK 500 2 ASN A 33 26.39 -160.09 REMARK 500 2 LYS A 36 -36.40 -154.64 REMARK 500 2 MET A 42 -38.49 -153.55 REMARK 500 2 GLU A 59 169.53 50.72 REMARK 500 2 ILE A 60 48.26 -152.06 REMARK 500 2 LEU A 71 98.62 -67.99 REMARK 500 2 ASN A 84 58.51 20.91 REMARK 500 2 ALA A 95 -43.24 -148.83 REMARK 500 2 VAL A 108 -56.12 -127.07 REMARK 500 2 THR A 111 -39.61 -149.41 REMARK 500 2 ALA A 112 172.99 54.50 REMARK 500 2 TYR A 122 94.70 -36.36 REMARK 500 2 GLN A 123 46.57 38.95 REMARK 500 2 ASP A 125 93.15 -45.14 REMARK 500 2 LEU A 143 48.54 -151.44 REMARK 500 2 TYR A 165 108.64 -57.73 REMARK 500 2 THR A 179 34.69 -143.26 REMARK 500 2 ASN A 194 -27.61 -144.98 REMARK 500 2 ASN A 202 102.92 47.47 REMARK 500 2 THR A 203 21.29 80.89 REMARK 500 3 ASN A 15 41.97 71.52 REMARK 500 REMARK 500 THIS ENTRY HAS 219 RAMACHANDRAN OUTLIERS. 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 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 39 OD1 REMARK 620 2 ASP A 39 OD2 45.7 REMARK 620 3 PHE A 41 O 61.5 93.7 REMARK 620 4 THR A 81 OG1 171.5 126.1 125.4 REMARK 620 5 ASN A 84 OD1 106.0 62.5 147.3 65.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 214 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 35 OD1 REMARK 620 2 ASP A 35 OD2 44.7 REMARK 620 3 ASN A 38 OD1 72.8 80.3 REMARK 620 4 GLU A 56 OE1 146.6 140.9 134.0 REMARK 620 5 GLU A 56 OE2 103.0 109.3 162.1 44.9 REMARK 620 6 SER A 87 OG 133.5 101.7 69.9 79.7 120.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 215 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 59 O REMARK 620 2 GLU A 59 OE1 56.9 REMARK 620 3 GLU A 59 OE2 81.9 44.8 REMARK 620 4 ASP A 61 OD1 124.0 77.3 87.2 REMARK 620 5 ASP A 61 OD2 118.9 107.5 131.4 44.3 REMARK 620 6 THR A 179 OG1 163.2 126.1 90.9 70.4 77.1 REMARK 620 7 GLN A 181 OE1 73.5 115.2 155.2 103.6 61.8 113.7 REMARK 620 8 ASN A 202 OD1 61.1 114.8 110.3 162.5 118.3 108.1 60.4 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 215 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YHP RELATED DB: PDB DBREF 2B1O A 2 213 UNP P54657 CAD1_DICDI 2 213 SEQRES 1 A 212 SER VAL ASP ALA ASN LYS VAL LYS PHE PHE PHE GLY LYS SEQRES 2 A 212 ASN CYS THR GLY GLU SER PHE GLU TYR ASN LYS GLY GLU SEQRES 3 A 212 THR VAL ARG PHE ASN ASN GLY ASP LYS TRP ASN ASP LYS SEQRES 4 A 212 PHE MET SER CYS LEU VAL GLY SER ASN VAL ARG CYS ASN SEQRES 5 A 212 ILE TRP GLU HIS ASN GLU ILE ASP THR PRO THR PRO GLY SEQRES 6 A 212 LYS PHE GLN GLU LEU ALA GLN GLY SER THR ASN ASN ASP SEQRES 7 A 212 LEU THR SER ILE ASN GLY LEU SER LYS PHE GLN VAL LEU SEQRES 8 A 212 PRO GLY ALA PHE GLN TRP ALA VAL ASP VAL LYS ILE VAL SEQRES 9 A 212 ASN LYS VAL ASN SER THR ALA GLY SER TYR GLU MET THR SEQRES 10 A 212 ILE THR PRO TYR GLN VAL ASP LYS VAL ALA CYS LYS ASP SEQRES 11 A 212 GLY ASP ASP PHE VAL GLN LEU PRO ILE PRO LYS LEU THR SEQRES 12 A 212 PRO PRO ASP SER GLU ILE VAL SER HIS LEU THR VAL ARG SEQRES 13 A 212 GLN THR HIS THR PRO TYR ASP TYR VAL VAL ASN GLY SER SEQRES 14 A 212 VAL TYR PHE LYS TYR SER PRO THR THR GLY GLN VAL THR SEQRES 15 A 212 VAL ILE LYS LYS ASP GLU THR PHE PRO LYS ASN MET THR SEQRES 16 A 212 VAL THR GLN ASP ASP ASN THR SER PHE ILE PHE ASN LEU SEQRES 17 A 212 ASN SER GLU LYS HET CA A 1 1 HET CA A 214 1 HET CA A 215 1 HETNAM CA CALCIUM ION FORMUL 2 CA 3(CA 2+) HELIX 1 1 LEU A 80 ASN A 84 5 5 SHEET 1 A 4 SER A 20 TYR A 23 0 SHEET 2 A 4 VAL A 8 PHE A 11 -1 N VAL A 8 O TYR A 23 SHEET 3 A 4 SER A 43 VAL A 46 -1 O SER A 43 N PHE A 11 SHEET 4 A 4 SER A 75 ASN A 77 -1 O ASN A 77 N CYS A 44 SHEET 1 B 4 GLU A 27 ARG A 30 0 SHEET 2 B 4 LYS A 88 PRO A 93 -1 O PHE A 89 N VAL A 29 SHEET 3 B 4 VAL A 50 TRP A 55 -1 N ARG A 51 O LEU A 92 SHEET 4 B 4 PHE A 68 LEU A 71 -1 O GLN A 69 N ILE A 54 SHEET 1 C 4 VAL A 136 ILE A 140 0 SHEET 2 C 4 TRP A 98 ASN A 106 -1 N TRP A 98 O ILE A 140 SHEET 3 C 4 SER A 204 LEU A 209 1 O PHE A 207 N LYS A 103 SHEET 4 C 4 MET A 195 ASP A 201 -1 N THR A 196 O ASN A 208 SHEET 1 D 5 VAL A 127 LYS A 130 0 SHEET 2 D 5 TYR A 115 PRO A 121 -1 N ILE A 119 O VAL A 127 SHEET 3 D 5 GLU A 149 GLN A 158 -1 O THR A 155 N THR A 118 SHEET 4 D 5 TYR A 165 SER A 176 -1 O VAL A 167 N VAL A 156 SHEET 5 D 5 GLN A 181 ILE A 185 -1 O ILE A 185 N TYR A 172 LINK CA CA A 1 OD1 ASP A 39 1555 1555 2.86 LINK CA CA A 1 OD2 ASP A 39 1555 1555 2.71 LINK CA CA A 1 O PHE A 41 1555 1555 2.94 LINK CA CA A 1 OG1 THR A 81 1555 1555 2.89 LINK CA CA A 1 OD1 ASN A 84 1555 1555 2.89 LINK OD1 ASP A 35 CA CA A 214 1555 1555 2.85 LINK OD2 ASP A 35 CA CA A 214 1555 1555 2.82 LINK OD1 ASN A 38 CA CA A 214 1555 1555 2.83 LINK OE1 GLU A 56 CA CA A 214 1555 1555 2.74 LINK OE2 GLU A 56 CA CA A 214 1555 1555 2.85 LINK O GLU A 59 CA CA A 215 1555 1555 2.88 LINK OE1 GLU A 59 CA CA A 215 1555 1555 2.89 LINK OE2 GLU A 59 CA CA A 215 1555 1555 2.69 LINK OD1 ASP A 61 CA CA A 215 1555 1555 2.85 LINK OD2 ASP A 61 CA CA A 215 1555 1555 2.84 LINK OG SER A 87 CA CA A 214 1555 1555 2.95 LINK OG1 THR A 179 CA CA A 215 1555 1555 2.78 LINK OE1 GLN A 181 CA CA A 215 1555 1555 2.73 LINK OD1 ASN A 202 CA CA A 215 1555 1555 2.86 CISPEP 1 THR A 144 PRO A 145 1 -4.75 CISPEP 2 THR A 161 PRO A 162 1 -6.73 CISPEP 3 THR A 144 PRO A 145 2 -1.84 CISPEP 4 THR A 161 PRO A 162 2 0.79 CISPEP 5 THR A 144 PRO A 145 3 -9.61 CISPEP 6 THR A 161 PRO A 162 3 3.07 CISPEP 7 THR A 144 PRO A 145 4 -7.76 CISPEP 8 THR A 161 PRO A 162 4 -0.40 CISPEP 9 THR A 144 PRO A 145 5 -3.19 CISPEP 10 THR A 161 PRO A 162 5 3.85 CISPEP 11 THR A 144 PRO A 145 6 -6.37 CISPEP 12 THR A 161 PRO A 162 6 4.27 CISPEP 13 THR A 144 PRO A 145 7 -5.90 CISPEP 14 THR A 161 PRO A 162 7 -6.60 CISPEP 15 THR A 144 PRO A 145 8 -5.48 CISPEP 16 THR A 161 PRO A 162 8 -1.40 CISPEP 17 THR A 144 PRO A 145 9 -3.50 CISPEP 18 THR A 161 PRO A 162 9 -4.21 CISPEP 19 THR A 144 PRO A 145 10 0.47 CISPEP 20 THR A 161 PRO A 162 10 4.38 SITE 1 AC1 4 ASP A 39 PHE A 41 THR A 81 ASN A 84 SITE 1 AC2 4 ASP A 35 ASN A 38 GLU A 56 SER A 87 SITE 1 AC3 5 GLU A 59 ASP A 61 THR A 179 GLN A 181 SITE 2 AC3 5 ASN A 202 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1