HEADER DNA BINDING PROTEIN 12-APR-04 1VF9 TITLE SOLUTION STRUCTURE OF HUMAN TRF2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TELOMERIC REPEAT BINDING FACTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN; COMPND 5 SYNONYM: TTAGGG REPEAT BINDING FACTOR 2, TELOMERIC DNA BINDING COMPND 6 PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET23B KEYWDS MYB, HELIX-TURN-HELIX, TELOMERE, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR Y.NISHIMURA,S.HANAOKA REVDAT 4 27-DEC-23 1VF9 1 REMARK REVDAT 3 02-MAR-22 1VF9 1 REMARK SEQADV REVDAT 2 24-FEB-09 1VF9 1 VERSN REVDAT 1 17-MAY-05 1VF9 0 JRNL AUTH S.HANAOKA,A.NAGADOI,Y.NISHIMURA JRNL TITL COMPARISON BETWEEN TRF2 AND TRF1 OF THEIR TELOMERIC JRNL TITL 2 DNA-BOUND STRUCTURES AND DNA-BINDING ACTIVITIES JRNL REF PROTEIN SCI. V. 14 119 2005 JRNL REFN ISSN 0961-8368 JRNL PMID 15608118 JRNL DOI 10.1110/PS.04983705 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.0, CNS 1.0 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 910 RESTRAINTS, 869 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 41 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1VF9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000006554. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.020M REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0-1.5MM TRF2 LABELED WITH 15N REMARK 210 AND 13C; 20MM POTASSIUM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O; 1.0-1.5MM TRF2 LABELED WITH REMARK 210 15N,AND DNA; 20MM POTASSIUM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HNHA; REMARK 210 3D_13N-SEPARATED_TOCSY; 3D_13C- REMARK 210 SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_TOCSY; 3D_13C- REMARK 210 SEPARATED_COSY; CBCACONH; CBCANH; REMARK 210 HNCO; HN(CA)CO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.98, CNS 1.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: 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: 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 THR A 442 -81.62 -65.26 REMARK 500 1 ASN A 443 37.63 -175.64 REMARK 500 1 THR A 445 52.34 -154.74 REMARK 500 1 LYS A 449 -71.49 -63.57 REMARK 500 1 THR A 451 -159.28 -134.13 REMARK 500 1 VAL A 480 -135.39 -67.75 REMARK 500 1 ASN A 481 44.32 -87.88 REMARK 500 1 THR A 483 -148.67 55.30 REMARK 500 2 GLU A 438 -47.50 -153.48 REMARK 500 2 ASP A 439 168.61 55.32 REMARK 500 2 THR A 441 -57.32 -156.52 REMARK 500 2 ASN A 443 73.82 -171.83 REMARK 500 2 LYS A 447 55.88 -90.28 REMARK 500 2 GLN A 448 51.91 -114.51 REMARK 500 2 ASN A 469 75.88 -116.29 REMARK 500 2 ASN A 481 26.73 48.70 REMARK 500 2 THR A 483 -156.97 56.21 REMARK 500 3 THR A 441 -68.12 -152.38 REMARK 500 3 ASN A 469 55.22 -99.19 REMARK 500 3 VAL A 480 -141.19 -63.69 REMARK 500 3 THR A 483 -149.72 56.60 REMARK 500 3 MET A 499 -44.23 -140.42 REMARK 500 4 THR A 441 -42.97 -142.51 REMARK 500 4 ASN A 443 -64.82 -131.04 REMARK 500 4 ILE A 444 72.61 52.78 REMARK 500 4 THR A 445 98.16 -56.03 REMARK 500 4 LYS A 446 44.48 -90.10 REMARK 500 4 GLN A 448 85.20 -62.44 REMARK 500 4 TRP A 450 -165.67 48.63 REMARK 500 4 ASN A 469 72.17 -118.44 REMARK 500 4 VAL A 480 -141.86 -63.24 REMARK 500 4 THR A 483 -174.12 55.05 REMARK 500 5 THR A 441 -51.13 -147.18 REMARK 500 5 THR A 442 -71.15 -77.06 REMARK 500 5 LYS A 447 -165.53 -69.29 REMARK 500 5 GLN A 448 74.15 52.85 REMARK 500 5 THR A 451 -165.42 -105.37 REMARK 500 5 ASN A 469 49.01 -102.11 REMARK 500 5 VAL A 480 -142.05 -63.85 REMARK 500 5 THR A 483 -152.66 54.74 REMARK 500 6 GLU A 438 -59.06 -162.81 REMARK 500 6 THR A 441 -40.84 -167.64 REMARK 500 6 THR A 442 30.48 -90.86 REMARK 500 6 ASN A 443 -46.22 -172.84 REMARK 500 6 THR A 445 91.70 52.40 REMARK 500 6 VAL A 480 -36.21 -130.77 REMARK 500 6 ASN A 481 37.93 -162.59 REMARK 500 6 THR A 483 -146.02 53.35 REMARK 500 6 MET A 499 19.84 -148.15 REMARK 500 7 GLU A 438 35.31 -161.47 REMARK 500 REMARK 500 THIS ENTRY HAS 186 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 482 0.21 SIDE CHAIN REMARK 500 1 ARG A 490 0.27 SIDE CHAIN REMARK 500 1 ARG A 492 0.29 SIDE CHAIN REMARK 500 1 ARG A 496 0.32 SIDE CHAIN REMARK 500 2 ARG A 482 0.22 SIDE CHAIN REMARK 500 2 ARG A 490 0.29 SIDE CHAIN REMARK 500 2 ARG A 492 0.30 SIDE CHAIN REMARK 500 2 ARG A 496 0.29 SIDE CHAIN REMARK 500 3 ARG A 482 0.26 SIDE CHAIN REMARK 500 3 ARG A 490 0.24 SIDE CHAIN REMARK 500 3 ARG A 492 0.29 SIDE CHAIN REMARK 500 3 ARG A 496 0.22 SIDE CHAIN REMARK 500 4 ARG A 482 0.32 SIDE CHAIN REMARK 500 4 ARG A 490 0.14 SIDE CHAIN REMARK 500 4 ARG A 492 0.28 SIDE CHAIN REMARK 500 4 ARG A 496 0.27 SIDE CHAIN REMARK 500 5 ARG A 482 0.21 SIDE CHAIN REMARK 500 5 ARG A 490 0.23 SIDE CHAIN REMARK 500 5 ARG A 492 0.18 SIDE CHAIN REMARK 500 5 ARG A 496 0.19 SIDE CHAIN REMARK 500 6 ARG A 482 0.21 SIDE CHAIN REMARK 500 6 ARG A 490 0.27 SIDE CHAIN REMARK 500 6 ARG A 492 0.28 SIDE CHAIN REMARK 500 6 ARG A 496 0.15 SIDE CHAIN REMARK 500 7 ARG A 482 0.31 SIDE CHAIN REMARK 500 7 ARG A 490 0.30 SIDE CHAIN REMARK 500 7 ARG A 492 0.28 SIDE CHAIN REMARK 500 7 ARG A 496 0.18 SIDE CHAIN REMARK 500 8 ARG A 482 0.16 SIDE CHAIN REMARK 500 8 ARG A 490 0.32 SIDE CHAIN REMARK 500 8 ARG A 492 0.27 SIDE CHAIN REMARK 500 8 ARG A 496 0.15 SIDE CHAIN REMARK 500 9 ARG A 482 0.32 SIDE CHAIN REMARK 500 9 ARG A 490 0.32 SIDE CHAIN REMARK 500 9 ARG A 492 0.16 SIDE CHAIN REMARK 500 9 ARG A 496 0.32 SIDE CHAIN REMARK 500 10 ARG A 482 0.27 SIDE CHAIN REMARK 500 10 ARG A 490 0.17 SIDE CHAIN REMARK 500 10 ARG A 492 0.28 SIDE CHAIN REMARK 500 10 ARG A 496 0.31 SIDE CHAIN REMARK 500 11 ARG A 482 0.28 SIDE CHAIN REMARK 500 11 ARG A 490 0.30 SIDE CHAIN REMARK 500 11 ARG A 492 0.28 SIDE CHAIN REMARK 500 11 ARG A 496 0.25 SIDE CHAIN REMARK 500 12 ARG A 482 0.32 SIDE CHAIN REMARK 500 12 ARG A 490 0.17 SIDE CHAIN REMARK 500 12 ARG A 492 0.29 SIDE CHAIN REMARK 500 12 ARG A 496 0.32 SIDE CHAIN REMARK 500 13 ARG A 482 0.29 SIDE CHAIN REMARK 500 13 ARG A 490 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 100 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VFC RELATED DB: PDB REMARK 900 DNA COMPLEX OF HUMAN TRF2 DBREF 1VF9 A 438 500 UNP Q15554 TERF2_HUMAN 438 500 SEQADV 1VF9 MET A 437 UNP Q15554 INITIATING METHIONINE SEQRES 1 A 64 MET GLU ASP SER THR THR ASN ILE THR LYS LYS GLN LYS SEQRES 2 A 64 TRP THR VAL GLU GLU SER GLU TRP VAL LYS ALA GLY VAL SEQRES 3 A 64 GLN LYS TYR GLY GLU GLY ASN TRP ALA ALA ILE SER LYS SEQRES 4 A 64 ASN TYR PRO PHE VAL ASN ARG THR ALA VAL MET ILE LYS SEQRES 5 A 64 ASP ARG TRP ARG THR MET LYS ARG LEU GLY MET ASN HELIX 1 1 THR A 451 GLY A 466 1 16 HELIX 2 2 ASN A 469 TYR A 477 1 9 HELIX 3 3 ALA A 484 GLY A 498 1 15 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