HEADER DNA BINDING PROTEIN 15-FEB-02 1ITY TITLE SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF HUMAN TRF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN; COMPND 5 SYNONYM: TELOMERIC REPEAT BINDING FACTOR 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TRF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET13A KEYWDS HELIX-TURN-HELIX, TELOMERES, DNA BINDING, MYB DOMAIN, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL KEYWDS 3 GENOMICS, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR T.NISHIKAWA,H.OKAMURA,A.NAGADOI,P.KONIG,D.RHODES,Y.NISHIMURA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 27-DEC-23 1ITY 1 REMARK REVDAT 3 23-FEB-22 1ITY 1 REMARK REVDAT 2 24-FEB-09 1ITY 1 VERSN REVDAT 1 06-MAR-02 1ITY 0 JRNL AUTH T.NISHIKAWA,H.OKAMURA,A.NAGADOI,P.KONIG,D.RHODES,Y.NISHIMURA JRNL TITL SOLUTION STRUCTURE OF A TELOMERIC DNA COMPLEX OF HUMAN TRF1 JRNL REF STRUCTURE V. 9 1237 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11738049 JRNL DOI 10.1016/S0969-2126(01)00688-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : EMBOSS 5.0 REMARK 3 AUTHORS : NAKAI, T., KIDERA, A., AND NAKAMURA, H. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE GENERATED BY 4D REMARK 3 SIMULATED ANNEALING WITH EMBOSS, BASED ON A TOTAL OF 916 REMARK 3 EXPERIMENTAL RESTRAINTS, 852 ARE NOE-DERIVED DISTANCE RESTRAINTS, REMARK 3 36 HYDROGEN RESTRAINTS AND 28 DIHEDRAL RESTRAINTS. 25 OUT OF REMARK 3 100 STRUCTURES WHICH HAVE THE LOWEST VIOLATION AND A LOW REMARK 3 ENERGIES WERE SELECTED FOR THE FINAL SET. REMARK 4 REMARK 4 1ITY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000005271. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5-2.5MM TRF1 U-15N, 13C, 50MM REMARK 210 PHOSPHATE BUFFER, 100MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNHA, 3D HNHB, 3D SEQUENTIAL REMARK 210 ASSIGNMENT PROTOCOL, 3D_15N_ REMARK 210 SEPARATED_NOESY, 3D_13C_ REMARK 210 SEPARATED_NOESY, 2D NOESY, 2D REMARK 210 TOCSY, 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX; AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL 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 LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 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 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 1-25 REMARK 465 RES C SSSEQI REMARK 465 THR A 371 REMARK 465 PRO A 372 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 14 ARG A 415 NE - CZ - NH2 ANGL. DEV. = -3.2 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 LYS A 374 71.33 -69.80 REMARK 500 1 HIS A 375 -35.50 172.92 REMARK 500 1 LYS A 379 118.64 74.15 REMARK 500 1 ASN A 402 53.91 -149.06 REMARK 500 1 ASN A 414 73.76 -154.73 REMARK 500 1 LYS A 431 43.96 -88.94 REMARK 500 1 LEU A 432 93.44 -11.48 REMARK 500 1 SER A 434 -135.51 56.50 REMARK 500 1 ASP A 436 24.80 -146.33 REMARK 500 2 ARG A 378 -100.16 49.38 REMARK 500 2 LYS A 379 36.39 -141.28 REMARK 500 2 GLN A 381 68.97 -69.74 REMARK 500 2 ALA A 382 52.75 -162.26 REMARK 500 2 TRP A 383 171.12 64.55 REMARK 500 2 ASN A 414 88.83 62.19 REMARK 500 2 LYS A 429 -72.25 -75.90 REMARK 500 2 LYS A 431 -21.59 179.55 REMARK 500 2 SER A 434 69.04 -153.77 REMARK 500 3 LYS A 374 -116.06 55.87 REMARK 500 3 HIS A 375 46.27 -157.35 REMARK 500 3 ARG A 376 173.25 71.55 REMARK 500 3 ARG A 378 -167.61 -179.39 REMARK 500 3 LYS A 379 129.63 -31.96 REMARK 500 3 ARG A 380 -168.57 -170.71 REMARK 500 3 TRP A 383 79.19 56.87 REMARK 500 3 ASN A 402 47.61 -76.21 REMARK 500 3 LEU A 432 62.09 67.09 REMARK 500 3 SER A 434 -86.45 -165.61 REMARK 500 3 SER A 435 -109.54 -122.72 REMARK 500 3 ASP A 436 -73.27 -150.02 REMARK 500 4 LYS A 374 -70.25 178.37 REMARK 500 4 HIS A 375 -175.09 59.94 REMARK 500 4 ARG A 376 115.29 66.27 REMARK 500 4 ARG A 380 98.54 -57.53 REMARK 500 4 ALA A 382 -131.83 55.19 REMARK 500 4 ASN A 414 83.50 61.31 REMARK 500 4 LEU A 430 -42.30 -178.15 REMARK 500 4 LYS A 431 -58.43 -19.11 REMARK 500 4 LEU A 432 32.30 -162.72 REMARK 500 5 ALA A 377 57.08 -162.56 REMARK 500 5 ARG A 380 34.71 -77.67 REMARK 500 5 ALA A 382 73.61 176.66 REMARK 500 5 LEU A 430 37.22 178.94 REMARK 500 5 LEU A 432 -56.14 -129.34 REMARK 500 5 ILE A 433 -87.06 -79.54 REMARK 500 6 ARG A 378 68.59 60.57 REMARK 500 6 TRP A 383 73.05 52.38 REMARK 500 6 ASN A 414 64.08 -161.02 REMARK 500 6 LYS A 431 -67.89 -159.55 REMARK 500 6 LEU A 432 -83.00 -169.73 REMARK 500 REMARK 500 THIS ENTRY HAS 204 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 12 ARG A 376 0.17 SIDE CHAIN REMARK 500 15 ARG A 415 0.12 SIDE CHAIN REMARK 500 18 ARG A 378 0.09 SIDE CHAIN REMARK 500 22 ARG A 423 0.11 SIDE CHAIN REMARK 500 24 ARG A 423 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BA5 RELATED DB: PDB REMARK 900 1BA5 CONTAINS THE SAME PROTEIN TRUNCATED IN N- AND C-TERMINI. REMARK 900 RELATED ID: MY_001000018.1 RELATED DB: TARGETDB DBREF 1ITY A 371 439 UNP P54274 TERF1_HUMAN 371 439 SEQRES 1 A 69 THR PRO GLU LYS HIS ARG ALA ARG LYS ARG GLN ALA TRP SEQRES 2 A 69 LEU TRP GLU GLU ASP LYS ASN LEU ARG SER GLY VAL ARG SEQRES 3 A 69 LYS TYR GLY GLU GLY ASN TRP SER LYS ILE LEU LEU HIS SEQRES 4 A 69 TYR LYS PHE ASN ASN ARG THR SER VAL MET LEU LYS ASP SEQRES 5 A 69 ARG TRP ARG THR MET LYS LYS LEU LYS LEU ILE SER SER SEQRES 6 A 69 ASP SER GLU ASP HELIX 1 1 LEU A 384 GLY A 399 1 16 HELIX 2 2 ASN A 402 TYR A 410 1 9 HELIX 3 3 THR A 416 LEU A 430 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