HEADER CELL CYCLE 31-JAN-02 1KXL TITLE SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN IN A COMPLEX WITH TITLE 2 SINGLE-STRANDED TELOMERIC DNA (DNA STRUCTURE NOT MODELED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION CONTROL PROTEIN 13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN (RESIDUES 497-694); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; 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: PET21A KEYWDS DNA-BINDING DOMAIN, TELOMERE, SINGLE-STRANDED DNA, OB FOLD, CELL KEYWDS 2 CYCLE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.M.MITTON-FRY,E.M.ANDERSON,D.S.WUTTKE REVDAT 3 23-FEB-22 1KXL 1 REMARK SEQADV REVDAT 2 24-FEB-09 1KXL 1 VERSN REVDAT 1 10-APR-02 1KXL 0 JRNL AUTH R.M.MITTON-FRY,E.M.ANDERSON,T.R.HUGHES,V.LUNDBLAD,D.S.WUTTKE JRNL TITL CONSERVED STRUCTURE FOR SINGLE-STRANDED TELOMERIC DNA JRNL TITL 2 RECOGNITION. JRNL REF SCIENCE V. 296 145 2002 JRNL REFN ISSN 0036-8075 JRNL PMID 11935027 JRNL DOI 10.1126/SCIENCE.1068799 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR 3.851 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DNA STRUCTURE NOT MODELED DUE TO REMARK 3 CHEMICAL SHIFT ASSIGNMENT AMBIGUITY. REMARK 4 REMARK 4 1KXL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015440. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 308 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : NULL; NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 4D_13C/15N- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG 3.3, X-PLOR 3.851 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: REPRESENTATIVE CONFORMER WAS STRUCTURE CLOSEST TO THE REMARK 210 MEAN. 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 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 O PHE A 182 H ARG A 186 1.50 REMARK 500 O GLU A 14 H GLN A 17 1.51 REMARK 500 O GLU A 90 H SER A 94 1.52 REMARK 500 O PRO A 156 H GLN A 158 1.56 REMARK 500 O GLY A 103 H ASP A 106 1.57 REMARK 500 O ASP A 93 H ARG A 97 1.58 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 80.85 55.98 REMARK 500 1 ARG A 8 -143.13 -74.17 REMARK 500 1 ILE A 13 -154.91 -146.43 REMARK 500 1 LEU A 18 -92.70 -40.19 REMARK 500 1 LEU A 20 -175.94 -56.14 REMARK 500 1 ASP A 21 -137.28 176.58 REMARK 500 1 THR A 22 -65.26 -102.76 REMARK 500 1 GLU A 24 -93.16 -7.86 REMARK 500 1 THR A 25 79.82 59.35 REMARK 500 1 LEU A 34 130.02 79.34 REMARK 500 1 PHE A 39 30.67 -97.80 REMARK 500 1 PHE A 44 -179.19 177.13 REMARK 500 1 SER A 50 -177.25 -176.55 REMARK 500 1 ASP A 51 -162.75 76.64 REMARK 500 1 PHE A 52 -51.65 75.01 REMARK 500 1 THR A 53 -137.39 -162.66 REMARK 500 1 GLN A 59 -150.18 34.01 REMARK 500 1 ASN A 60 -143.93 -123.23 REMARK 500 1 LEU A 62 99.57 71.76 REMARK 500 1 ASP A 64 175.40 66.29 REMARK 500 1 LEU A 67 -162.19 36.20 REMARK 500 1 ILE A 68 -71.92 -64.58 REMARK 500 1 LYS A 73 126.13 -37.84 REMARK 500 1 LEU A 74 178.66 -52.25 REMARK 500 1 ASN A 77 50.76 -94.57 REMARK 500 1 GLU A 78 -35.76 -159.06 REMARK 500 1 PHE A 100 -89.26 -123.78 REMARK 500 1 ASN A 101 -28.93 176.77 REMARK 500 1 ASN A 109 26.82 40.18 REMARK 500 1 ARG A 111 -74.96 -45.50 REMARK 500 1 SER A 116 -24.88 167.36 REMARK 500 1 GLN A 117 54.40 -98.63 REMARK 500 1 TYR A 118 -51.26 -134.12 REMARK 500 1 LYS A 129 176.50 170.66 REMARK 500 1 TYR A 131 -62.26 -144.70 REMARK 500 1 LYS A 134 -156.47 -122.76 REMARK 500 1 CYS A 142 99.04 -178.14 REMARK 500 1 PRO A 146 -89.07 -71.54 REMARK 500 1 HIS A 147 -39.57 -166.42 REMARK 500 1 SER A 155 173.45 -52.93 REMARK 500 1 SER A 157 -59.39 68.01 REMARK 500 1 TYR A 181 51.48 -143.44 REMARK 500 1 ARG A 187 -29.89 -36.66 REMARK 500 1 PHE A 189 154.76 63.80 REMARK 500 2 MET A 6 -142.02 33.75 REMARK 500 2 ALA A 7 44.86 173.87 REMARK 500 2 ASP A 10 74.12 167.87 REMARK 500 2 ILE A 13 -152.99 -157.52 REMARK 500 2 GLU A 14 91.62 175.78 REMARK 500 2 PHE A 15 -76.67 54.37 REMARK 500 REMARK 500 THIS ENTRY HAS 422 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 0.31 SIDE CHAIN REMARK 500 1 ARG A 65 0.22 SIDE CHAIN REMARK 500 1 ARG A 97 0.24 SIDE CHAIN REMARK 500 1 ARG A 105 0.31 SIDE CHAIN REMARK 500 1 ARG A 111 0.28 SIDE CHAIN REMARK 500 1 ARG A 140 0.29 SIDE CHAIN REMARK 500 1 ARG A 163 0.29 SIDE CHAIN REMARK 500 1 ARG A 168 0.32 SIDE CHAIN REMARK 500 1 ARG A 172 0.30 SIDE CHAIN REMARK 500 1 ARG A 180 0.30 SIDE CHAIN REMARK 500 1 ARG A 187 0.28 SIDE CHAIN REMARK 500 2 ARG A 8 0.25 SIDE CHAIN REMARK 500 2 ARG A 65 0.24 SIDE CHAIN REMARK 500 2 ARG A 97 0.17 SIDE CHAIN REMARK 500 2 ARG A 105 0.30 SIDE CHAIN REMARK 500 2 ARG A 111 0.31 SIDE CHAIN REMARK 500 2 ARG A 140 0.29 SIDE CHAIN REMARK 500 2 ARG A 163 0.11 SIDE CHAIN REMARK 500 2 ARG A 168 0.22 SIDE CHAIN REMARK 500 2 ARG A 172 0.29 SIDE CHAIN REMARK 500 2 ARG A 180 0.30 SIDE CHAIN REMARK 500 2 ARG A 186 0.28 SIDE CHAIN REMARK 500 3 ARG A 8 0.28 SIDE CHAIN REMARK 500 3 ARG A 65 0.32 SIDE CHAIN REMARK 500 3 ARG A 97 0.31 SIDE CHAIN REMARK 500 3 ARG A 105 0.28 SIDE CHAIN REMARK 500 3 ARG A 111 0.20 SIDE CHAIN REMARK 500 3 ARG A 140 0.28 SIDE CHAIN REMARK 500 3 ARG A 163 0.31 SIDE CHAIN REMARK 500 3 ARG A 168 0.22 SIDE CHAIN REMARK 500 3 ARG A 172 0.30 SIDE CHAIN REMARK 500 3 ARG A 186 0.19 SIDE CHAIN REMARK 500 3 ARG A 187 0.31 SIDE CHAIN REMARK 500 4 ARG A 8 0.32 SIDE CHAIN REMARK 500 4 ARG A 65 0.18 SIDE CHAIN REMARK 500 4 ARG A 97 0.22 SIDE CHAIN REMARK 500 4 ARG A 105 0.27 SIDE CHAIN REMARK 500 4 ARG A 111 0.31 SIDE CHAIN REMARK 500 4 ARG A 140 0.13 SIDE CHAIN REMARK 500 4 ARG A 163 0.29 SIDE CHAIN REMARK 500 4 ARG A 168 0.30 SIDE CHAIN REMARK 500 4 ARG A 172 0.31 SIDE CHAIN REMARK 500 4 ARG A 180 0.20 SIDE CHAIN REMARK 500 4 ARG A 186 0.11 SIDE CHAIN REMARK 500 4 ARG A 187 0.20 SIDE CHAIN REMARK 500 5 ARG A 8 0.32 SIDE CHAIN REMARK 500 5 ARG A 65 0.31 SIDE CHAIN REMARK 500 5 ARG A 97 0.18 SIDE CHAIN REMARK 500 5 ARG A 105 0.27 SIDE CHAIN REMARK 500 5 ARG A 111 0.20 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 115 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1KXL A 2 199 UNP P32797 CDC13_YEAST 497 694 SEQADV 1KXL MET A 1 UNP P32797 CLONING ARTIFACT 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 LYS A 86 LYS A 98 1 13 HELIX 2 2 GLY A 103 GLN A 108 1 6 HELIX 3 3 GLN A 149 ALA A 154 1 6 HELIX 4 4 SER A 157 GLY A 174 1 18 HELIX 5 5 GLY A 174 TYR A 181 1 8 HELIX 6 6 TYR A 181 ARG A 186 1 6 SHEET 1 A 3 LYS A 26 MET A 30 0 SHEET 2 A 3 CYS A 122 LYS A 129 -1 O ILE A 126 N ILE A 28 SHEET 3 A 3 ASN A 136 VAL A 139 -1 O ASN A 136 N LYS A 129 SHEET 1 B 3 LYS A 26 MET A 30 0 SHEET 2 B 3 CYS A 122 LYS A 129 -1 O ILE A 126 N ILE A 28 SHEET 3 B 3 GLU A 143 PRO A 144 -1 O GLU A 143 N LYS A 123 SHEET 1 C 3 SER A 36 SER A 38 0 SHEET 2 C 3 PHE A 44 PHE A 49 -1 O VAL A 48 N SER A 36 SHEET 3 C 3 PHE A 80 TYR A 85 -1 O ALA A 82 N PHE A 47 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