10 20 30 40 50 60 70 80 1J5K - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION/DNA 13-MAY-02 1J5K
TITLE COMPLEX OF THE KH3 DOMAIN OF HNRNP K WITH A SINGLE_STRANDED TITLE 2 10MER DNA OLIGONUCLEOTIDE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KH3 DOMAIN, RESIDUES 379-463, NUMBERED 5-89; COMPND 5 SYNONYM: HNRNP K, DC-STRETCH BINDING PROTEIN, CSBP, COMPND 6 TRANSFORMATION UPREGULATED NUCLEAR PROTEIN, TUNP; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*AP*TP*AP*T*TP*CP*CP*CP*TP*C)-3'; COMPND 10 CHAIN: B; COMPND 11 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_STRAIN: BE23; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES
KEYWDS SINGLE-STRANDED DNA BINDING PROTEIN, TRANSCRIPTION FACTOR, KEYWDS 2 HNRNP K, CT ELEMENT, C-MYC ONCOGENE, TRANSCRIPTION/DNA KEYWDS 3 COMPLEX
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,D.T.BRADDOCK
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 JRNL TITL 2 SINGLE-STRANDED DNA RECOGNITION BY KH DOMAINS: JRNL TITL 3 SOLUTION STRUCTURE OF A COMPLEX BETWEEN HNRNP K JRNL TITL 4 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 1
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- REMARK 3 302) 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 REMARK 3 (KUSZEWSKI ET AL. J. MAGN. RESON 125, 171-177 (1997)) AND BASE- REMARK 3 BASE POSITIONAL (KUSZEWSKI ET AL. J AM CHEM SOC 123, 3903-3918 REMARK 3 (2001)) 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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB001639.
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 REMARK 210 FOR 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 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: 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 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 SEQRES 1 B 10 DA DT DA DT DT DC DC DC DT DC
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