Header list of 1j5k.pdb file
Complete list - 23 20 Bytes
HEADER TRANSCRIPTION/DNA 13-MAY-02 1J5K
TITLE COMPLEX OF THE KH3 DOMAIN OF HNRNP K WITH A SINGLE_STRANDED 10MER DNA
TITLE 2 OLIGONUCLEOTIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*AP*TP*AP*T*TP*CP*CP*CP*TP*C)-3';
COMPND 3 CHAIN: B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K;
COMPND 7 CHAIN: A;
COMPND 8 FRAGMENT: KH3 DOMAIN, RESIDUES 379-463, NUMBERED 5-89;
COMPND 9 SYNONYM: HNRNP K, DC-STRETCH BINDING PROTEIN, CSBP, TRANSFORMATION
COMPND 10 UPREGULATED NUCLEAR PROTEIN, TUNP;
COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 5 ORGANISM_COMMON: HUMAN;
SOURCE 6 ORGANISM_TAXID: 9606;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BE23;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS SINGLE-STRANDED DNA BINDING PROTEIN, TRANSCRIPTION FACTOR, HNRNP K,
KEYWDS 2 CT ELEMENT, C-MYC ONCOGENE, TRANSCRIPTION-DNA COMPLEX
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,D.T.BRADDOCK
REVDAT 3 23-FEB-22 1J5K 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1J5K 1 VERSN
REVDAT 1 10-JUL-02 1J5K 0
JRNL AUTH D.T.BRADDOCK,J.L.BABER,D.LEVENS,G.M.CLORE
JRNL TITL MOLECULAR BASIS OF SEQUENCE-SPECIFIC SINGLE-STRANDED DNA
JRNL TITL 2 RECOGNITION BY KH DOMAINS: SOLUTION STRUCTURE OF A COMPLEX
JRNL TITL 3 BETWEEN HNRNP K KH3 AND SINGLE-STRANDED DNA.
JRNL REF EMBO J. V. 21 3476 2002
JRNL REFN ISSN 0261-4189
JRNL PMID 12093748
JRNL DOI 10.1093/EMBOJ/CDF352
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR NIH (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH)
REMARK 3 AUTHORS : CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION
REMARK 3 ANGLE SPACE (SCHWIETERS AND CLORE (2001) J MAGN RESON 152, 288-302)
REMARK 3 AGAINST A TARGET FUNCTION COMPRISING THE EXPERIMENTAL NMR
REMARK 3 RESTRAINTS (NOE-DERIVED INTERPROTON DISTANCE, TORSION ANGLE,
REMARK 3 13CALPHA/13CBETA SHIFTS AND DIPOLAR COUPLINGS). THE NON-BONDED
REMARK 3 CONTACTS IN THE TARGET FUNCTION ARE REPRESENTED BY A QUARTIC VAN
REMARK 3 DER WAALS REPULSION TERM, SUPPLEMENTED BY TORSION ANGLE (KUSZEWSKI
REMARK 3 ET AL. J. MAGN. RESON 125, 171-177 (1997)) AND BASE-BASE
REMARK 3 POSITIONAL (KUSZEWSKI ET AL. J AM CHEM SOC 123, 3903-3918 (2001))
REMARK 3 DATABASE POTENTIALS OF MEAN FORCE.
REMARK 3
REMARK 3 IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF
REMARK 3 THE 125 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
REMARK 3 ABOUT THE MEAN COORDINATE POSITIONS: RESIDUES 1-9 AND
REMARK 3 86-89 OF THE PROTEIN ARE DISORDERED IN THE COMPLEX.
REMARK 3 ALTHOUGH THE SINGLE-STRANDED DNA IS B-LIKE, THE
REMARK 3 COORDINATES OF THOSE PORTIONS OF THE SS-DNA NOT IN
REMARK 3 CONTACT WITH THE PROTEIN COULD NOT BE ACCURATELY DETERMINED
REMARK 3 (BASES 101-104 AND 110). THEREFORE ONLY THE COORDINATES OF
REMARK 3 RESIDUES 10-85 AND NUCLEOTIDES 105-109 ARE PRESENTED.
REMARK 3
REMARK 3 SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON
REMARK 3 1986 EXPERIMENTAL NMR RESTRAINTS
REMARK 3 DISTANCES 1289
REMARK 3 TORSION ANGLES 266
REMARK 3 13CA/CB SHIFTS 144
REMARK 3 1DNH DIPOLARS IN PEG/HEXANOL 63
REMARK 3 1DNC' DIPOLARS IN PEG/HEXANOL 44
REMARK 3 2DHNC' DIPOLARS IN PEG/HEXANOL 40
REMARK 3 1DNH DIPOLARS IN PHAGE PF1 56
REMARK 3 1DNC' DIPOLARS IN PHAGE PF1 42
REMARK 3 2DHNC' DIPOLARS IN PHAGE PF1 42
REMARK 3
REMARK 3 BREAKDOWN OF INTRAMOLECULAR PROTEIN DISTANCE RESTRAINTS
REMARK 3 INTRARESIDUE 315
REMARK 3 SEQUENTIAL 282
REMARK 3 MEDIUM RANGE 197
REMARK 3 LONG RANGE 300
REMARK 3 BACKBONE H-BONDS 54 RESTRAINTS FOR 27 H-BONDS
REMARK 3 INTRA-DNA DISTANCES 68
REMARK 3 INTERMOLECULAR DISTANCES 73
REMARK 4
REMARK 4 1J5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-02.
REMARK 100 THE DEPOSITION ID IS D_1000001639.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308
REMARK 210 PH : 6.80
REMARK 210 IONIC STRENGTH : 50 MM SODIUM PHOSPHATE
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : (1) TRIPLE RESONANCE FOR
REMARK 210 ASSIGNMENT OF PROTEIN; (2)
REMARK 210 QUANTITATIVE J CORRELATION FOR
REMARK 210 COUPLING CONSTANTS; (3) 3D, 4D
REMARK 210 HETERONUCLEAR SEPARATED,
REMARK 210 FILTERED NOE EXPTS; (4) 2D 12C-
REMARK 210 FILTERED EXPERIMENTS FOR DNA
REMARK 210 ASSIGNMENTS; (5) IPAP EXPTS FOR
REMARK 210 DIPOLAR COUPLINGS
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : DMX; DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XPLOR_NIH
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 125
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : REGULARIZED MEAN STRUCTURE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
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 RES C SSSEQI
REMARK 465 DA B 101
REMARK 465 DT B 102
REMARK 465 DA B 103
REMARK 465 DT B 104
REMARK 465 DC B 110
REMARK 465 GLY A 1
REMARK 465 SER A 2
REMARK 465 HIS A 3
REMARK 465 MET A 4
REMARK 465 SER A 5
REMARK 465 TYR A 6
REMARK 465 GLY A 7
REMARK 465 ASP A 8
REMARK 465 LEU A 9
REMARK 465 GLY A 86
REMARK 465 LYS A 87
REMARK 465 PHE A 88
REMARK 465 PHE A 89
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 RES CSSEQI ATOMS
REMARK 470 DT B 105 P OP1 OP2
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 O3' DC B 108 HH12 ARG A 40 1.47
REMARK 500 O GLN A 67 H GLN A 71 1.56
REMARK 500
REMARK 500 REMARK: NULL
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 DT B 105 C4' - C3' - C2' ANGL. DEV. = 8.0 DEGREES
REMARK 500 DC B 106 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES
REMARK 500 DC B 107 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES
REMARK 500 DC B 108 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES
REMARK 500 DT B 109 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES
REMARK 500 DT B 109 O4' - C1' - C2' ANGL. DEV. = 3.1 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 ASP A 23 -15.33 -49.51
REMARK 500 GLU A 57 40.12 -105.66
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1J5K A 5 89 UNP P61978 ROK_HUMAN 379 463
DBREF 1J5K B 101 110 PDB 1J5K 1J5K 101 110
SEQADV 1J5K GLY A 1 UNP P61978 CLONING ARTIFACT
SEQADV 1J5K SER A 2 UNP P61978 CLONING ARTIFACT
SEQADV 1J5K HIS A 3 UNP P61978 CLONING ARTIFACT
SEQADV 1J5K MET A 4 UNP P61978 CLONING ARTIFACT
SEQRES 1 B 10 DA DT DA DT DT DC DC DC DT DC
SEQRES 1 A 89 GLY SER HIS MET SER TYR GLY ASP LEU GLY GLY PRO ILE
SEQRES 2 A 89 ILE THR THR GLN VAL THR ILE PRO LYS ASP LEU ALA GLY
SEQRES 3 A 89 SER ILE ILE GLY LYS GLY GLY GLN ARG ILE LYS GLN ILE
SEQRES 4 A 89 ARG HIS GLU SER GLY ALA SER ILE LYS ILE ASP GLU PRO
SEQRES 5 A 89 LEU GLU GLY SER GLU ASP ARG ILE ILE THR ILE THR GLY
SEQRES 6 A 89 THR GLN ASP GLN ILE GLN ASN ALA GLN TYR LEU LEU GLN
SEQRES 7 A 89 ASN SER VAL LYS GLN TYR SER GLY LYS PHE PHE
HELIX 1 1 LYS A 22 GLY A 30 1 9
HELIX 2 2 GLY A 33 SER A 43 1 11
HELIX 3 3 GLN A 67 SER A 85 1 19
SHEET 1 A 3 ILE A 13 PRO A 21 0
SHEET 2 A 3 ASP A 58 THR A 66 -1 O ILE A 61 N VAL A 18
SHEET 3 A 3 SER A 46 ILE A 49 -1 N LYS A 48 O THR A 62
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
Complete list - 23 20 Bytes