Header list of 1ity.pdb file
Complete list - b 23 2 Bytes
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 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
Complete list - b 23 2 Bytes