HEADER CELL ADHESION 06-APR-01 1IE5 TITLE NMR STRUCTURE OF THE THIRD IMMUNOGLOBULIN DOMAIN FROM THE NEURAL CELL TITLE 2 ADHESION MOLECULE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL CELL ADHESION MOLECULE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIRD IMMUNOGLOBULIN DOMAIN, RESIDUES 183-288; COMPND 5 SYNONYM: N-CAM; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 ORGAN: BRAIN; 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: PET3D KEYWDS INTERMEDIATE IMMUNOGLOBULIN FOLD, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.R.ATKINS,J.CHUNG,S.DEECHONGKIT,E.B.LITTLE,G.M.EDELMAN,P.E.WRIGHT, AUTHOR 2 B.A.CUNNINGHAM,H.J.DYSON REVDAT 3 23-FEB-22 1IE5 1 REMARK SEQADV REVDAT 2 24-FEB-09 1IE5 1 VERSN REVDAT 1 08-AUG-01 1IE5 0 JRNL AUTH A.R.ATKINS,J.CHUNG,S.DEECHONGKIT,E.B.LITTLE,G.M.EDELMAN, JRNL AUTH 2 P.E.WRIGHT,B.A.CUNNINGHAM,H.J.DYSON JRNL TITL SOLUTION STRUCTURE OF THE THIRD IMMUNOGLOBULIN DOMAIN OF THE JRNL TITL 2 NEURAL CELL ADHESION MOLECULE N-CAM: CAN SOLUTION STUDIES JRNL TITL 3 DEFINE THE MECHANISM OF HOMOPHILIC BINDING? JRNL REF J.MOL.BIOL. V. 311 161 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11469865 JRNL DOI 10.1006/JMBI.2001.4861 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.8, AMBER 7 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 1461 UNIQUE REMARK 3 NOE-DERIVED RESTRAINTS, 393 AMBIGUOUS NOE-DERIVED RESTRAINTS, REMARK 3 AND 131 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1IE5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013197. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NO SALT REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM IGIII U-15N,13C; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHB; CGCN, REMARK 210 CGCO REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.5, NMRVIEW 3, SANE 1 REMARK 210 METHOD USED : SIMULATED ANNEALING RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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: 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 1 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 TRP A 47 CA - CB - CG ANGL. DEV. = 11.8 DEGREES REMARK 500 5 TRP A 47 CA - CB - CG ANGL. DEV. = 12.1 DEGREES REMARK 500 7 TRP A 47 CA - CB - CG ANGL. DEV. = 12.4 DEGREES REMARK 500 9 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 TRP A 47 CA - CB - CG ANGL. DEV. = 12.0 DEGREES REMARK 500 17 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 17 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 20 TRP A 47 CA - CB - CG ANGL. DEV. = 12.9 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 ILE A 4 -49.02 -153.88 REMARK 500 1 GLN A 5 30.26 -147.20 REMARK 500 1 SER A 19 -40.75 73.76 REMARK 500 1 ASP A 50 -9.34 69.72 REMARK 500 1 ILE A 54 39.24 -96.47 REMARK 500 1 ASP A 58 -23.10 -153.90 REMARK 500 1 GLU A 60 11.53 -152.31 REMARK 500 1 LYS A 62 48.92 -157.10 REMARK 500 1 SER A 70 24.63 -143.05 REMARK 500 1 LYS A 76 74.98 27.23 REMARK 500 1 ASP A 78 -37.10 -137.04 REMARK 500 1 LYS A 79 -31.84 165.75 REMARK 500 1 ALA A 106 46.49 -93.09 REMARK 500 2 GLN A 5 -157.64 -160.58 REMARK 500 2 CYS A 35 64.91 -117.71 REMARK 500 2 ASP A 50 -32.49 70.42 REMARK 500 2 GLU A 55 88.33 -23.72 REMARK 500 2 ASP A 58 -28.65 -157.74 REMARK 500 2 GLU A 61 -51.24 -22.60 REMARK 500 2 LYS A 62 47.55 -154.57 REMARK 500 2 SER A 70 17.22 -152.04 REMARK 500 2 GLU A 71 92.94 -63.00 REMARK 500 2 ALA A 106 53.31 -106.24 REMARK 500 3 GLN A 5 29.24 -156.36 REMARK 500 3 VAL A 8 -45.86 -151.83 REMARK 500 3 SER A 13 78.00 -153.40 REMARK 500 3 ASN A 26 -1.32 72.69 REMARK 500 3 CYS A 35 73.82 -114.00 REMARK 500 3 GLU A 55 85.65 -13.35 REMARK 500 3 ASP A 58 -30.94 -155.40 REMARK 500 3 LYS A 62 47.92 -154.53 REMARK 500 3 SER A 70 28.80 -144.09 REMARK 500 3 ALA A 106 48.36 -103.52 REMARK 500 4 VAL A 8 -38.74 -156.04 REMARK 500 4 SER A 13 50.46 -140.70 REMARK 500 4 ASN A 26 -6.13 69.00 REMARK 500 4 GLU A 42 133.27 -37.82 REMARK 500 4 ASP A 50 -17.91 71.07 REMARK 500 4 ILE A 54 42.51 -103.23 REMARK 500 4 ASP A 58 -20.05 -158.81 REMARK 500 4 LYS A 62 48.94 -157.63 REMARK 500 5 GLN A 5 31.12 -82.95 REMARK 500 5 VAL A 8 -30.64 -138.94 REMARK 500 5 ASN A 26 -3.17 72.74 REMARK 500 5 GLU A 42 108.17 -27.10 REMARK 500 5 LYS A 49 51.89 -100.93 REMARK 500 5 ASP A 50 -2.76 77.06 REMARK 500 5 ILE A 54 40.31 -106.43 REMARK 500 5 ASP A 58 -4.78 -153.17 REMARK 500 5 GLU A 60 12.16 -161.43 REMARK 500 REMARK 500 THIS ENTRY HAS 213 RAMACHANDRAN OUTLIERS. 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 7 TYR A 85 0.07 SIDE CHAIN REMARK 500 17 ARG A 17 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN IS A FRAGMENT CONSISTING OF THE THIRD REMARK 999 IMMUNOGLOBULIN DOMAIN. THE RESIDUE NUMBERS THAT ARE REMARK 999 REFERRED TO (183-288) ARE FOR THE PROCESSED PROTEIN, REMARK 999 AFTER REMOVAL OF THE SIGNAL SEQUENCE. THE SIGNAL REMARK 999 SEQUENCE IS INCLUDED IN THE SWISSPROT DATABASE, HENCE REMARK 999 THE DISCREPANCY IN THE NUMBERING. THE CORRECT MATCH REMARK 999 WITH THE DATABASE NUMBERING IS WITH RESIDUES 202 -307, REMARK 999 WITH AN ADDITIONAL N-TERMINAL GLYCINE INTRODUCING IN REMARK 999 THE CLONING. DBREF 1IE5 A 2 107 UNP P13590 NCAM1_CHICK 202 307 SEQADV 1IE5 GLY A 1 UNP P13590 CLONING ARTIFACT SEQRES 1 A 107 GLY LYS ASP ILE GLN VAL ILE VAL ASN VAL PRO PRO SER SEQRES 2 A 107 VAL ARG ALA ARG GLN SER THR MET ASN ALA THR ALA ASN SEQRES 3 A 107 LEU SER GLN SER VAL THR LEU ALA CYS ASP ALA ASP GLY SEQRES 4 A 107 PHE PRO GLU PRO THR MET THR TRP THR LYS ASP GLY GLU SEQRES 5 A 107 PRO ILE GLU GLN GLU ASP ASN GLU GLU LYS TYR SER PHE SEQRES 6 A 107 ASN TYR ASP GLY SER GLU LEU ILE ILE LYS LYS VAL ASP SEQRES 7 A 107 LYS SER ASP GLU ALA GLU TYR ILE CYS ILE ALA GLU ASN SEQRES 8 A 107 LYS ALA GLY GLU GLN ASP ALA THR ILE HIS LEU LYS VAL SEQRES 9 A 107 PHE ALA LYS SHEET 1 A 2 VAL A 10 ALA A 16 0 SHEET 2 A 2 CYS A 35 PHE A 40 -1 O ASP A 36 N ARG A 15 SHEET 1 B 5 THR A 20 THR A 24 0 SHEET 2 B 5 GLU A 95 PHE A 105 1 O HIS A 101 N MET A 21 SHEET 3 B 5 ALA A 83 GLU A 90 -1 O ALA A 83 N LEU A 102 SHEET 4 B 5 THR A 44 LYS A 49 -1 N THR A 44 O GLU A 90 SHEET 5 B 5 GLU A 52 PRO A 53 -1 O GLU A 52 N LYS A 49 SHEET 1 C 3 GLN A 29 LEU A 33 0 SHEET 2 C 3 LEU A 72 VAL A 77 -1 N LEU A 72 O LEU A 33 SHEET 3 C 3 TYR A 63 SER A 64 -1 O SER A 64 N ILE A 73 SSBOND 1 CYS A 35 CYS A 87 1555 1555 2.01 CISPEP 1 PHE A 40 PRO A 41 1 -8.04 CISPEP 2 PHE A 40 PRO A 41 2 -7.56 CISPEP 3 PHE A 40 PRO A 41 3 0.71 CISPEP 4 PHE A 40 PRO A 41 4 -4.32 CISPEP 5 PHE A 40 PRO A 41 5 -2.20 CISPEP 6 PHE A 40 PRO A 41 6 -10.58 CISPEP 7 PHE A 40 PRO A 41 7 10.01 CISPEP 8 PHE A 40 PRO A 41 8 4.56 CISPEP 9 PHE A 40 PRO A 41 9 -9.51 CISPEP 10 PHE A 40 PRO A 41 10 -7.59 CISPEP 11 PHE A 40 PRO A 41 11 4.36 CISPEP 12 PHE A 40 PRO A 41 12 -2.52 CISPEP 13 PHE A 40 PRO A 41 13 -10.43 CISPEP 14 PHE A 40 PRO A 41 14 -4.14 CISPEP 15 PHE A 40 PRO A 41 15 0.88 CISPEP 16 PHE A 40 PRO A 41 16 0.10 CISPEP 17 PHE A 40 PRO A 41 17 -10.71 CISPEP 18 PHE A 40 PRO A 41 18 -10.10 CISPEP 19 PHE A 40 PRO A 41 19 0.00 CISPEP 20 PHE A 40 PRO A 41 20 -8.01 CRYST1 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