HEADER RNA BINDING PROTEIN 07-JAN-99 1KHM TITLE C-TERMINAL KH DOMAIN OF HNRNP K (KH3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HNRNP K); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL KH DOMAIN, RESIDUES 379-463 OF FULL LENGTH HNRNP COMPND 5 K; COMPND 6 SYNONYM: KH3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-3 KEYWDS HNRNP K, KH DOMAIN, THREE-DIMENSIONAL STRUCTURE, C-MYC, DIPOLAR KEYWDS 2 COUPLING, DNA-BINDING, RNA-BINDING, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.BABER,D.LIBUTTI,D.LEVENS,N.TJANDRA REVDAT 5 27-DEC-23 1KHM 1 REMARK REVDAT 4 23-FEB-22 1KHM 1 REMARK SEQADV REVDAT 3 24-FEB-09 1KHM 1 VERSN REVDAT 2 01-APR-03 1KHM 1 JRNL REVDAT 1 12-JAN-00 1KHM 0 JRNL AUTH J.L.BABER,D.LIBUTTI,D.LEVENS,N.TJANDRA JRNL TITL HIGH PRECISION SOLUTION STRUCTURE OF THE C-TERMINAL KH JRNL TITL 2 DOMAIN OF HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K, A C-MYC JRNL TITL 3 TRANSCRIPTION FACTOR. JRNL REF J.MOL.BIOL. V. 289 949 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10369774 JRNL DOI 10.1006/JMBI.1999.2818 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING REMARK 3 PROTOCOL OF REMARK 3 NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM REMARK 3 XPLOR 3.1 ( REMARK 3 BRUNGER) MODIFIED TO INCORPORATE DIPOLAR COUPLING RESTRAINTS REMARK 3 (UNPUBLISHED). REMARK 3 THE 3D STRUCTURE OF THE C-TERMINAL G26R MUTANT KH DOMAIN OF HNRNP REMARK 3 K WAS SOLVED REMARK 3 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR. IT IS REMARK 3 BASED ON REMARK 3 1567 EXPERIMENTAL RESTRAINTS: 448 INTRARESIDUE, 322 SEQUENTIAL (|I- REMARK 3 J|=1), 198 REMARK 3 MEDIUM RANGE (1 < |I-J| >=5) AND 279 LONG RANGE (|I-J| >5) REMARK 3 DISTANCE RESTRAINTS; REMARK 3 55 DISTANCE RESTRAINTS FOR 28 HYDROGEN BONDS; 49 DNH, 59 DCH, 48 REMARK 3 DC'N, AND 53 REMARK 3 DCAC' DIPOLAR COUPLING RESTRAINTS; 56 PHI-ANGLE RESTRAINTS FROM HN- REMARK 3 HA COUPLING REMARK 3 CONSTANTS. THE 20 STRUCTURES ARE ARRANGED IN ORDER OF INCREASING REMARK 3 OVERALL REMARK 3 ENERGY WITH MODEL 1 THE LOWEST. MODEL 9 HAS THE SMALLEST BACKBONE REMARK 3 PAIRWISE RMS REMARK 3 TO THE AVERAGE STRUCTURE. REMARK 4 REMARK 4 1KHM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007125. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 5 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST OVERALL ENERGY 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: 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 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 TYR A 84 HG SER A 85 1.47 REMARK 500 O GLN A 83 H SER A 85 1.51 REMARK 500 O SER A 80 H GLN A 83 1.54 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 PRO A 3 33.83 -70.17 REMARK 500 1 ASN A 4 69.96 -154.06 REMARK 500 1 SER A 5 103.16 -164.06 REMARK 500 1 TYR A 6 -176.27 54.06 REMARK 500 1 ASP A 8 28.00 46.83 REMARK 500 1 TYR A 84 55.05 -66.63 REMARK 500 1 PHE A 88 98.71 51.32 REMARK 500 2 PRO A 3 -167.32 -67.29 REMARK 500 2 ASN A 4 110.26 -168.73 REMARK 500 2 SER A 5 53.44 -165.56 REMARK 500 2 GLN A 34 -26.84 -36.24 REMARK 500 2 SER A 56 94.89 -163.81 REMARK 500 2 TYR A 84 60.76 -65.81 REMARK 500 2 SER A 85 8.48 54.40 REMARK 500 2 PHE A 88 107.09 56.39 REMARK 500 3 SER A 2 70.76 52.25 REMARK 500 3 PRO A 3 -166.56 -68.39 REMARK 500 3 ASP A 8 91.66 52.19 REMARK 500 3 SER A 56 102.23 -163.96 REMARK 500 3 GLU A 57 49.67 -70.21 REMARK 500 3 TYR A 84 86.89 -53.80 REMARK 500 3 PHE A 88 101.30 52.51 REMARK 500 4 TYR A 6 42.66 -165.33 REMARK 500 4 ASP A 8 115.43 58.86 REMARK 500 4 GLN A 34 -28.23 -36.26 REMARK 500 4 GLU A 57 31.07 -144.02 REMARK 500 4 TYR A 84 42.77 -69.34 REMARK 500 4 SER A 85 7.58 59.02 REMARK 500 4 PHE A 88 45.80 -171.67 REMARK 500 5 SER A 5 -11.15 -155.84 REMARK 500 5 TYR A 6 3.56 -172.00 REMARK 500 5 ASP A 8 89.63 -45.49 REMARK 500 5 GLN A 34 -29.63 -34.02 REMARK 500 5 GLU A 57 33.58 -144.63 REMARK 500 5 SER A 85 10.77 52.37 REMARK 500 5 PHE A 88 40.95 -162.00 REMARK 500 6 ASP A 8 143.57 60.48 REMARK 500 6 GLN A 34 -27.11 -36.53 REMARK 500 6 SER A 85 58.66 -171.57 REMARK 500 6 PHE A 88 81.55 -178.03 REMARK 500 7 SER A 2 71.64 50.32 REMARK 500 7 TYR A 6 33.90 -74.79 REMARK 500 7 ASP A 8 167.21 -42.92 REMARK 500 7 GLN A 34 -26.95 -38.93 REMARK 500 7 GLU A 57 34.80 -142.46 REMARK 500 7 TYR A 84 81.67 -58.34 REMARK 500 7 SER A 85 53.05 82.68 REMARK 500 7 PHE A 88 -7.92 -52.56 REMARK 500 8 SER A 2 71.26 -168.16 REMARK 500 8 ASN A 4 13.35 -167.94 REMARK 500 REMARK 500 THIS ENTRY HAS 171 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1KHM A 1 89 UNP P61978 ROK_HUMAN 375 463 SEQADV 1KHM SER A 2 UNP P61978 GLY 376 CONFLICT SEQADV 1KHM PRO A 3 UNP P61978 ARG 377 CONFLICT SEQADV 1KHM ASN A 4 UNP P61978 GLY 378 CONFLICT SEQADV 1KHM ARG A 26 UNP P61978 GLY 400 SEE REMARK 999 SEQRES 1 A 89 GLY SER PRO ASN 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 ARG 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 GLY A 7 GLY A 10 5 4 HELIX 2 2 LYS A 22 ILE A 29 1 8 HELIX 3 3 GLN A 34 SER A 43 1 10 HELIX 4 4 GLN A 67 GLN A 83 1 17 SHEET 1 A 3 ILE A 14 PRO A 21 0 SHEET 2 A 3 ASP A 58 GLY A 65 -1 N GLY A 65 O ILE A 14 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 MODEL 1