Header list of 1j4w.pdb file
Complete list - 27 20 Bytes
HEADER TRANSCRIPTION/DNA 30-NOV-01 1J4W
TITLE COMPLEX OF THE KH3 AND KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29MER
TITLE 2 DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-
COMPND 3 D(*GP*TP*A*TP*AP*TP*TP*CP*CP*CP*TP*CP*GP*GP*G*AP*TP*TP*TP*TP*TP*TP*AP
COMPND 4 *TP*TP*TP*TP*GP*T)-3');
COMPND 5 CHAIN: B;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: FUSE BINDING PROTEIN;
COMPND 10 CHAIN: A;
COMPND 11 FRAGMENT: RESIDUES 278-447, NUMBERERED 5-174. KH3 AND KH4 DOMAINS.;
COMPND 12 SYNONYM: FBP, FAR UPSTREAM BINDING ELEMENT PROTEIN;
COMPND 13 ENGINEERED: YES;
COMPND 14 MUTATION: 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, FBP, FUSE
KEYWDS 2 ELEMENT, C-MYC ONCOGENE, TRANSCRIPTION-DNA COMPLEX
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,D.T.BRADDOCK
REVDAT 3 27-OCT-21 1J4W 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1J4W 1 VERSN
REVDAT 1 06-MAR-02 1J4W 0
JRNL AUTH D.T.BRADDOCK,J.M.LOUIS,J.L.BABER,D.LEVENS,G.M.CLORE
JRNL TITL STRUCTURE AND DYNAMICS OF KH DOMAINS FROM FBP BOUND TO
JRNL TITL 2 SINGLE-STRANDED DNA.
JRNL REF NATURE V. 415 1051 2002
JRNL REFN ISSN 0028-0836
JRNL PMID 11875576
JRNL DOI 10.1038/4151051A
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, 3J
REMARK 3 COUPLING, 13CALPHA/13CBETA SHIFTS AND DIPOLAR COUPLINGS). THE NON-
REMARK 3 BONDED CONTACTS IN THE TARGET FUNCTION ARE REPRESENTED BY A
REMARK 3 QUARTIC VAN DER WAALS REPULSION TERM, SUPPLEMENTED BY TORSION
REMARK 3 ANGLE (KUSZEWSKI ET AL. J. MAGN. RESON 125, 171-177 (1997)) 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 80 INDIVIDUAL SIMULATED ANNEALING STRUCTURES (FOR
REMARK 3 EACH HALF OF THE COMPLEX) ABOUT THE MEAN COORDINATE
REMARK 3 POSITIONS: RESIDUES 75-103 OF THE PROTEIN ARE
REMARK 3 DISORDERED IN THE COMPLEX. ALTHOUGH THE SINGLE-STRANDED
REMARK 3 DNA IS B-LIKE, THE COORDINATES OF THOSE PORTIONS OF THE
REMARK 3 SS-DNA NOT IN CONTACT WITH THE PROTEIN COULD NOT BE
REMARK 3 ACCURATELY DETERMINED (BASES 201-203, 212-215 AND
REMARK 3 223-229). THEREFORE THE COORDINATES ARE PRESENTED IN
REMARK 3 TWO HALVES: THE KH3 HALF OF THE COMPLEX (RESIDUES 1-74
REMARK 3 OF THE PROTEIN AND BASES 216-222 OF THE SS-DNA) AND THE
REMARK 3 KH4 HALF OF THE COMPLEX (RESIDUES 104-174 OF THE
REMARK 3 PROTEIN AND BASES 204-211 OF THE SS-DNA). THE
REMARK 3 COORDINATE ACCURACY IS CALCULATED FOR THE TWO HALVES OF
REMARK 3 THE COMPLEX SEPARATELY. THE APPROXIMATE ORIENTATION OF
REMARK 3 AND SEPARATION BETWEEN THE TWO DOMAINS COULD BE DERIVED
REMARK 3 FROM ANALYSIS OF HETERONUCLEAR RELAXATION MEASUREMENTS.
REMARK 3 THE ORIENTATIONS OF THE TWO HALVES OF THE COMPLEX IN
REMARK 3 THESE COORDINATES REFLECTS THE RESULTS OF THE
REMARK 3 RELAXATION MEASUREMENTS. THE AVERAGE ORIENTATION OF THE
REMARK 3 TWO HALVES OF THE COMPLEX IS PARALLEL WITH AN AVERAGE
REMARK 3 INTERHELICAL ANGLE OF ABOUT 1 DEGREE BETWEEN THE THIRD
REMARK 3 HELIX OF EACH DOMAIN. THE OVERALL ROTATIONAL
REMARK 3 CORRELATION TIME OF THE COMPLEX IS 21.5 NS WITH A
REMARK 3 DIFFUSION ANISOTROPY OF 1.85. THE TIME SCALE FOR THE
REMARK 3 INTERDOMAIN MOTIONS IS AROUND 4 NS AND THE TWO DOMAINS
REMARK 3 WOBBLE INDEPENDENTLY IN CONES WITH SEMI-ANGLES OF ABOUT
REMARK 3 30 DEGREES. THE OVERALL LENGTH OF THE COMPLEX IS ABOUT
REMARK 3 100 ANGSTROMS AND THE SEPARATION BETWEEN THE TWO HALVES
REMARK 3 OF THE COMPLEX IS AROUND 35 ANGSTROMS. THE RESTRAINED
REMARK 3 REGULARIZED MEAN STRUCTURE FOR THE TWO HALVES OF THE
REMARK 3 COMPLEX IS OBTAINED BY RESTRAINED REGULARIZATION OF THE
REMARK 3 AVERAGE COORDINATES AGAINST THE SAME TARGET FUNCTION
REMARK 3 USED TO CALCULATE THE SIMULATED ANNEALING STRUCTURES.
REMARK 3
REMARK 3 SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON
REMARK 3 3153 EXPERIMENTAL NMR RESTRAINTS
REMARK 3 KH3 HALF KH4 HALF
REMARK 3 DISTANCES 1095 949
REMARK 3 TORSION ANGLES 244 261
REMARK 3 3JHNA COUPLINGS 33 36
REMARK 3 13CA/CB SHIFTS 120 121
REMARK 3 1DNH DIPOLARS 61 61
REMARK 3 1DNC' DIPOLARS 47 39
REMARK 3 2DHNC' DIPOLARS 46 40
REMARK 3
REMARK 3 BREAKDOWN OF INTRAMOLECULAR PROTEIN DISTANCE RESTRAINTS
REMARK 3 INTRARESIDUE 157 169
REMARK 3 SEQUENTIAL 274 216
REMARK 3 MEDIUM RANGE 247 155
REMARK 3 LONG RANGE 260 216
REMARK 3 BACKBONE H-BONDS 33 36
REMARK 3
REMARK 3 INTRA-DNA DISTANCES 41 53
REMARK 3 INTERMOLECULAR DISTANCES 50 68
REMARK 4
REMARK 4 1J4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-01.
REMARK 100 THE DEPOSITION ID IS D_1000001616.
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 WERE MEASURED
REMARK 210 IN A LIQUID CRYSTALLINE MEDIUM
REMARK 210 OF PHAGE FD (25 MG/ML)
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : DMX AND 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 : 80
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 DG B 201
REMARK 465 DT B 202
REMARK 465 DA B 203
REMARK 465 DC B 212
REMARK 465 DG B 213
REMARK 465 DG B 214
REMARK 465 DG B 215
REMARK 465 DA B 223
REMARK 465 DT B 224
REMARK 465 DT B 225
REMARK 465 DT B 226
REMARK 465 DT B 227
REMARK 465 DG B 228
REMARK 465 DT B 229
REMARK 465 ALA A 75
REMARK 465 GLY A 76
REMARK 465 ASN A 77
REMARK 465 PRO A 78
REMARK 465 GLY A 79
REMARK 465 GLY A 80
REMARK 465 PRO A 81
REMARK 465 GLY A 82
REMARK 465 PRO A 83
REMARK 465 GLY A 84
REMARK 465 GLY A 85
REMARK 465 ARG A 86
REMARK 465 GLY A 87
REMARK 465 ARG A 88
REMARK 465 GLY A 89
REMARK 465 ARG A 90
REMARK 465 GLY A 91
REMARK 465 GLN A 92
REMARK 465 GLY A 93
REMARK 465 ASN A 94
REMARK 465 TRP A 95
REMARK 465 ASN A 96
REMARK 465 MET A 97
REMARK 465 GLY A 98
REMARK 465 PRO A 99
REMARK 465 PRO A 100
REMARK 465 GLY A 101
REMARK 465 GLY A 102
REMARK 465 LEU A 103
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 204 P OP1 OP2 O5'
REMARK 470 DA B 216 P OP1 OP2 O5'
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 O ILE A 28 H ALA A 32 1.55
REMARK 500 O GLU A 171 H ILE A 174 1.56
REMARK 500 O ILE A 25 H GLN A 29 1.59
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 PRO A 40 160.84 -38.22
REMARK 500 THR A 44 -12.62 60.49
REMARK 500 PRO A 46 49.99 -77.68
REMARK 500 PRO A 143 109.50 -48.58
REMARK 500 GLU A 171 -79.42 -53.94
REMARK 500 GLU A 172 -17.46 -34.42
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1J4W A 5 174 UNP Q96AE4 FUBP1_HUMAN 278 447
DBREF 1J4W B 201 229 PDB 1J4W 1J4W 201 229
SEQADV 1J4W GLY A 1 UNP Q96AE4 CLONING ARTIFACT
SEQADV 1J4W SER A 2 UNP Q96AE4 CLONING ARTIFACT
SEQADV 1J4W HIS A 3 UNP Q96AE4 CLONING ARTIFACT
SEQADV 1J4W MET A 4 UNP Q96AE4 CLONING ARTIFACT
SEQADV 1J4W ALA A 59 UNP Q96AE4 CYS 332 ENGINEERED MUTATION
SEQRES 1 B 29 DG DT DA DT DA DT DT DC DC DC DT DC DG
SEQRES 2 B 29 DG DG DA DT DT DT DT DT DT DA DT DT DT
SEQRES 3 B 29 DT DG DT
SEQRES 1 A 174 GLY SER HIS MET ILE ASP VAL PRO ILE PRO ARG PHE ALA
SEQRES 2 A 174 VAL GLY ILE VAL ILE GLY ARG ASN GLY GLU MET ILE LYS
SEQRES 3 A 174 LYS ILE GLN ASN ASP ALA GLY VAL ARG ILE GLN PHE LYS
SEQRES 4 A 174 PRO ASP ASP GLY THR THR PRO GLU ARG ILE ALA GLN ILE
SEQRES 5 A 174 THR GLY PRO PRO ASP ARG ALA GLN HIS ALA ALA GLU ILE
SEQRES 6 A 174 ILE THR ASP LEU LEU ARG SER VAL GLN ALA GLY ASN PRO
SEQRES 7 A 174 GLY GLY PRO GLY PRO GLY GLY ARG GLY ARG GLY ARG GLY
SEQRES 8 A 174 GLN GLY ASN TRP ASN MET GLY PRO PRO GLY GLY LEU GLN
SEQRES 9 A 174 GLU PHE ASN PHE ILE VAL PRO THR GLY LYS THR GLY LEU
SEQRES 10 A 174 ILE ILE GLY LYS GLY GLY GLU THR ILE LYS SER ILE SER
SEQRES 11 A 174 GLN GLN SER GLY ALA ARG ILE GLU LEU GLN ARG ASN PRO
SEQRES 12 A 174 PRO PRO ASN ALA ASP PRO ASN MET LYS LEU PHE THR ILE
SEQRES 13 A 174 ARG GLY THR PRO GLN GLN ILE ASP TYR ALA ARG GLN LEU
SEQRES 14 A 174 ILE GLU GLU LYS ILE
HELIX 1 1 ARG A 11 GLY A 19 1 9
HELIX 2 2 GLY A 22 GLY A 33 1 12
HELIX 3 3 PRO A 55 GLN A 74 1 20
HELIX 4 4 LYS A 114 GLY A 120 1 7
HELIX 5 5 GLY A 123 GLY A 134 1 12
HELIX 6 6 THR A 159 ILE A 174 1 16
SHEET 1 A 3 HIS A 3 PRO A 10 0
SHEET 2 A 3 GLU A 47 GLY A 54 -1 O ALA A 50 N VAL A 7
SHEET 3 A 3 ARG A 35 LYS A 39 -1 N GLN A 37 O GLN A 51
SHEET 1 B 3 GLU A 105 PRO A 111 0
SHEET 2 B 3 MET A 151 ARG A 157 -1 O PHE A 154 N PHE A 108
SHEET 3 B 3 ARG A 136 GLN A 140 -1 N ARG A 136 O ARG A 157
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 - 27 20 Bytes