Header list of 1s40.pdb file
Complete list - r 2 2 Bytes
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
Complete list - r 2 2 Bytes