HEADER CELL CYCLE/DNA 14-JAN-04 1S40 TITLE SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH A TITLE 2 SINGLE-STRANDED TELOMERIC DNA 11-MER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CELL DIVISION CONTROL PROTEIN 13; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: DNA-BINDING DOMAIN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 5 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 6 ORGANISM_TAXID: 4932; SOURCE 7 GENE: CDC13, YDL220C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SSDNA, SINGLE-STRANDED NUCLEIC ACID, RECOGNITION, SPECIFICITY, CDC13, KEYWDS 2 OB-FOLD, TELOMERE, CELL CYCLE-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.M.MITTON-FRY,E.M.ANDERSON,D.L.THEOBALD,L.W.GLUSTROM,D.S.WUTTKE REVDAT 3 02-MAR-22 1S40 1 REMARK SEQADV REVDAT 2 24-FEB-09 1S40 1 VERSN REVDAT 1 04-MAY-04 1S40 0 JRNL AUTH R.M.MITTON-FRY,E.M.ANDERSON,D.L.THEOBALD,L.W.GLUSTROM, JRNL AUTH 2 D.S.WUTTKE JRNL TITL STRUCTURAL BASIS FOR TELOMERIC SINGLE-STRANDED DNA JRNL TITL 2 RECOGNITION BY YEAST CDC13 JRNL REF J.MOL.BIOL. V. 338 241 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15066429 JRNL DOI 10.1016/J.JMB.2004.01.063 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S40 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021338. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150MM NACL, 100MM NA2SO4 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8-1.5MM UNLABELED, 15N-LABELED REMARK 210 OR 13C,15N-LABELED PROTEIN; 0.9- REMARK 210 1.7MM SSDNA; 50MM IMIDAZOLE-D4, REMARK 210 PH OR PD* 7.0; 150MM NACL; 100MM REMARK 210 NA2SO4; 0.02% NAN3; 2MM DTT-D10 REMARK 210 IN 10% D2O/90% H2O OR 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; 4D_13C/15N- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; ISOTOPE REMARK 210 FILTERED NOESY; SELECT-FILTERED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 MATRIX RELAXATION, TORSION ANGLE REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: MODELS SUPERIMPOSED USING DOUGLAS THEOBALD'S THESEUS REMARK 210 PROGRAM FOR MULTIPLE SUPERPOSITIONS, VARIANCE-WEIGHTED REMARK 210 SIMULTANEOUS SUPERPOSITIONING. THE FINAL WEIGHTED RMSD FROM THE REMARK 210 MEAN IS 0.64152A OVER ALL ALPHA-CARBON ATOMS 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 MET A 3 REMARK 465 SER A 4 REMARK 465 HIS A 192 REMARK 465 ARG A 193 REMARK 465 ASN A 194 REMARK 465 GLY A 195 REMARK 465 SER A 196 REMARK 465 HIS A 197 REMARK 465 LEU A 198 REMARK 465 ALA A 199 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 H2'' DG B 7 O5' DT B 8 1.22 REMARK 500 O ASN A 125 H ARG A 140 1.51 REMARK 500 O LYS A 129 H ASN A 136 1.54 REMARK 500 O ARG A 186 H PHE A 189 1.56 REMARK 500 O4' DG B 9 H72 DT B 10 1.58 REMARK 500 O ILE A 28 H ILE A 126 1.59 REMARK 500 O ARG A 168 H ARG A 172 1.59 REMARK 500 O GLN A 149 H SER A 152 1.60 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 ALA A 7 103.97 -171.60 REMARK 500 1 PRO A 11 -165.45 -75.40 REMARK 500 1 ILE A 13 -159.89 -154.41 REMARK 500 1 GLU A 14 82.65 -172.03 REMARK 500 1 PHE A 15 -74.20 60.30 REMARK 500 1 LEU A 18 -150.92 -55.92 REMARK 500 1 LEU A 20 -177.30 -47.65 REMARK 500 1 THR A 22 -81.43 -40.06 REMARK 500 1 GLU A 24 -156.81 -71.50 REMARK 500 1 THR A 25 150.52 148.93 REMARK 500 1 LYS A 26 -160.25 -177.59 REMARK 500 1 SER A 38 89.77 -150.05 REMARK 500 1 PHE A 44 -161.38 173.63 REMARK 500 1 SER A 46 130.72 -33.60 REMARK 500 1 ASP A 51 -140.08 -170.20 REMARK 500 1 PHE A 52 -143.30 -99.09 REMARK 500 1 THR A 53 -173.88 45.73 REMARK 500 1 GLN A 59 -152.87 32.73 REMARK 500 1 ASN A 60 -166.00 -122.92 REMARK 500 1 TYR A 63 -155.15 48.25 REMARK 500 1 ARG A 65 47.87 35.54 REMARK 500 1 TYR A 66 94.14 -26.02 REMARK 500 1 LEU A 67 171.25 -43.91 REMARK 500 1 TYR A 85 145.18 -39.44 REMARK 500 1 ASN A 101 6.91 59.94 REMARK 500 1 ARG A 111 -98.51 -96.62 REMARK 500 1 ASP A 112 -173.86 -67.75 REMARK 500 1 GLU A 141 -160.23 -126.03 REMARK 500 1 CYS A 142 58.68 175.24 REMARK 500 1 PRO A 146 -87.89 -69.88 REMARK 500 1 HIS A 147 -40.33 -147.14 REMARK 500 1 SER A 155 -58.64 177.83 REMARK 500 1 SER A 157 -56.86 67.75 REMARK 500 1 TYR A 181 44.77 -140.66 REMARK 500 1 ARG A 187 -92.56 42.30 REMARK 500 1 PRO A 190 40.68 -79.58 REMARK 500 2 ALA A 7 87.61 -55.18 REMARK 500 2 ARG A 8 -161.04 -116.21 REMARK 500 2 LYS A 9 -177.66 49.49 REMARK 500 2 ASP A 10 119.31 168.25 REMARK 500 2 PHE A 15 -77.07 57.69 REMARK 500 2 LEU A 18 -154.79 -51.86 REMARK 500 2 LEU A 20 -166.86 -52.65 REMARK 500 2 THR A 22 -85.23 -78.24 REMARK 500 2 GLU A 24 -152.15 -55.88 REMARK 500 2 THR A 25 100.06 150.11 REMARK 500 2 LYS A 26 -167.60 -116.99 REMARK 500 2 LEU A 34 107.50 48.94 REMARK 500 2 PHE A 44 -168.52 168.01 REMARK 500 2 ASP A 51 -79.07 -121.31 REMARK 500 REMARK 500 THIS ENTRY HAS 384 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 1 ARG A 8 0.26 SIDE CHAIN REMARK 500 1 ARG A 65 0.08 SIDE CHAIN REMARK 500 1 ARG A 97 0.26 SIDE CHAIN REMARK 500 1 ARG A 105 0.32 SIDE CHAIN REMARK 500 1 ARG A 111 0.20 SIDE CHAIN REMARK 500 1 ARG A 140 0.18 SIDE CHAIN REMARK 500 1 ARG A 168 0.14 SIDE CHAIN REMARK 500 1 ARG A 172 0.21 SIDE CHAIN REMARK 500 1 ARG A 180 0.20 SIDE CHAIN REMARK 500 1 ARG A 186 0.31 SIDE CHAIN REMARK 500 1 ARG A 187 0.26 SIDE CHAIN REMARK 500 2 ARG A 8 0.26 SIDE CHAIN REMARK 500 2 ARG A 65 0.31 SIDE CHAIN REMARK 500 2 ARG A 97 0.27 SIDE CHAIN REMARK 500 2 ARG A 105 0.32 SIDE CHAIN REMARK 500 2 ARG A 111 0.24 SIDE CHAIN REMARK 500 2 ARG A 140 0.17 SIDE CHAIN REMARK 500 2 ARG A 163 0.23 SIDE CHAIN REMARK 500 2 ARG A 168 0.32 SIDE CHAIN REMARK 500 2 ARG A 172 0.32 SIDE CHAIN REMARK 500 2 ARG A 186 0.26 SIDE CHAIN REMARK 500 2 ARG A 187 0.29 SIDE CHAIN REMARK 500 3 ARG A 8 0.32 SIDE CHAIN REMARK 500 3 ARG A 65 0.11 SIDE CHAIN REMARK 500 3 ARG A 97 0.31 SIDE CHAIN REMARK 500 3 ARG A 105 0.19 SIDE CHAIN REMARK 500 3 ARG A 111 0.19 SIDE CHAIN REMARK 500 3 ARG A 140 0.12 SIDE CHAIN REMARK 500 3 ARG A 163 0.12 SIDE CHAIN REMARK 500 3 ARG A 168 0.32 SIDE CHAIN REMARK 500 3 ARG A 172 0.32 SIDE CHAIN REMARK 500 3 ARG A 180 0.31 SIDE CHAIN REMARK 500 3 ARG A 186 0.15 SIDE CHAIN REMARK 500 3 ARG A 187 0.22 SIDE CHAIN REMARK 500 4 ARG A 8 0.32 SIDE CHAIN REMARK 500 4 ARG A 65 0.31 SIDE CHAIN REMARK 500 4 ARG A 105 0.27 SIDE CHAIN REMARK 500 4 ARG A 111 0.29 SIDE CHAIN REMARK 500 4 ARG A 140 0.27 SIDE CHAIN REMARK 500 4 ARG A 163 0.28 SIDE CHAIN REMARK 500 4 ARG A 168 0.28 SIDE CHAIN REMARK 500 4 ARG A 172 0.30 SIDE CHAIN REMARK 500 4 ARG A 180 0.31 SIDE CHAIN REMARK 500 4 ARG A 186 0.24 SIDE CHAIN REMARK 500 4 ARG A 187 0.29 SIDE CHAIN REMARK 500 5 ARG A 8 0.31 SIDE CHAIN REMARK 500 5 ARG A 65 0.23 SIDE CHAIN REMARK 500 5 ARG A 97 0.22 SIDE CHAIN REMARK 500 5 ARG A 105 0.32 SIDE CHAIN REMARK 500 5 ARG A 111 0.16 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 115 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KXL RELATED DB: PDB REMARK 900 SAME PROTEIN CONSTRUCT WITHOUT DNA MODELED DBREF 1S40 A 2 199 UNP P32797 CDC13_YEAST 497 694 DBREF 1S40 B 1 11 PDB 1S40 1S40 1 11 SEQADV 1S40 MET A 1 UNP P32797 CLONING ARTIFACT SEQRES 1 B 11 DG DT DG DT DG DG DG DT DG DT DG SEQRES 1 A 199 MET ARG MET SER LYS MET ALA ARG LYS ASP PRO THR ILE SEQRES 2 A 199 GLU PHE CYS GLN LEU GLY LEU ASP THR PHE GLU THR LYS SEQRES 3 A 199 TYR ILE THR MET PHE GLY MET LEU VAL SER CYS SER PHE SEQRES 4 A 199 ASP LYS PRO ALA PHE ILE SER PHE VAL PHE SER ASP PHE SEQRES 5 A 199 THR LYS ASN ASP ILE VAL GLN ASN TYR LEU TYR ASP ARG SEQRES 6 A 199 TYR LEU ILE ASP TYR GLU ASN LYS LEU GLU LEU ASN GLU SEQRES 7 A 199 GLY PHE LYS ALA ILE MET TYR LYS ASN GLN PHE GLU THR SEQRES 8 A 199 PHE ASP SER LYS LEU ARG LYS ILE PHE ASN ASN GLY LEU SEQRES 9 A 199 ARG ASP LEU GLN ASN GLY ARG ASP GLU ASN LEU SER GLN SEQRES 10 A 199 TYR GLY ILE VAL CYS LYS MET ASN ILE LYS VAL LYS MET SEQRES 11 A 199 TYR ASN GLY LYS LEU ASN ALA ILE VAL ARG GLU CYS GLU SEQRES 12 A 199 PRO VAL PRO HIS SER GLN ILE SER SER ILE ALA SER PRO SEQRES 13 A 199 SER GLN CYS GLU HIS LEU ARG LEU PHE TYR GLN ARG ALA SEQRES 14 A 199 PHE LYS ARG ILE GLY GLU SER ALA ILE SER ARG TYR PHE SEQRES 15 A 199 GLU GLU TYR ARG ARG PHE PHE PRO ILE HIS ARG ASN GLY SEQRES 16 A 199 SER HIS LEU ALA HELIX 1 1 GLU A 14 LEU A 18 5 5 HELIX 2 2 TYR A 85 ASN A 101 1 17 HELIX 3 3 GLY A 103 GLN A 108 1 6 HELIX 4 4 GLN A 149 ALA A 154 1 6 HELIX 5 5 SER A 157 ILE A 173 1 17 HELIX 6 6 GLY A 174 TYR A 181 1 8 HELIX 7 7 TYR A 181 ARG A 186 1 6 SHEET 1 A 5 GLY A 79 ALA A 82 0 SHEET 2 A 5 SER A 46 SER A 50 -1 N PHE A 47 O ALA A 82 SHEET 3 A 5 LYS A 26 SER A 38 -1 N SER A 38 O SER A 46 SHEET 4 A 5 VAL A 121 VAL A 128 -1 O ILE A 126 N ILE A 28 SHEET 5 A 5 ILE A 138 VAL A 139 -1 O ILE A 138 N LYS A 127 SHEET 1 B 5 GLY A 79 ALA A 82 0 SHEET 2 B 5 SER A 46 SER A 50 -1 N PHE A 47 O ALA A 82 SHEET 3 B 5 LYS A 26 SER A 38 -1 N SER A 38 O SER A 46 SHEET 4 B 5 VAL A 121 VAL A 128 -1 O ILE A 126 N ILE A 28 SHEET 5 B 5 GLU A 143 PRO A 144 -1 O GLU A 143 N LYS A 123 SHEET 1 C 2 MET A 130 TYR A 131 0 SHEET 2 C 2 LYS A 134 LEU A 135 -1 O LYS A 134 N TYR A 131 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