PDB Short entry for 1MBK HEADER DNA BINDING PROTEIN 19-MAY-95 1MBK TITLE MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYB PROTO-ONCOGENE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: GENE C-MYB, NMR, 50 STRUCTURES; ENGINEERED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090 KEYWDS PROTOONCOGENE PRODUCT, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 50 AUTHOR K.OGATA,S.MORIKAWA,H.NAKAMURA,H.HOJO,S.YOSHIMURA,R.ZHANG,S.AIMOTO, AUTHOR 2 Y.AMETANI,Z.HIRATA,A.SARAI,S.ISHII,Y.NISHIMURA REVDAT 4 29-FEB-12 1MBK 1 JRNL VERSN REVDAT 3 24-FEB-09 1MBK 1 VERSN REVDAT 2 01-APR-03 1MBK 1 JRNL REVDAT 1 31-JUL-95 1MBK 0 JRNL AUTH K.OGATA,S.MORIKAWA,H.NAKAMURA,H.HOJO,S.YOSHIMURA,R.ZHANG, JRNL AUTH 2 S.AIMOTO,Y.AMETANI,Z.HIRATA,A.SARAI,S.ISHII,Y.NISHIMURA JRNL TITL COMPARISON OF THE FREE AND DNA-COMPLEXED FORMS OF THE JRNL TITL 2 DNA-BINDING DOMAIN FROM C-MYB. JRNL REF NAT.STRUCT.BIOL. V. 2 309 1995 JRNL REFN ISSN 1072-8368 JRNL PMID 7796266 JRNL DOI 10.1038/NSB0495-309 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.OGATA,S.MORIKAWA,H.NAKAMURA,A.SEKIKAWA,T.INOUE,H.KANAI, REMARK 1 AUTH 2 A.SARAI,S.ISHII,Y.NISHIMURA REMARK 1 TITL SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB REMARK 1 TITL 2 DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 79 639 1994 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.OGATA,H.HOJO,S.AIMOTO,T.NAKAI,H.NAKAMURA,A.SARAI,S.ISHII, REMARK 1 AUTH 2 Y.NISHIMURA REMARK 1 TITL SOLUTION STRUCTURE OF A DNA-BINDING UNIT OF MYB: A REMARK 1 TITL 2 HELIX-TURN-HELIX-RELATED MOTIF WITH CONSERVED TRYPTOPHANS REMARK 1 TITL 3 FORMING A HYDROPHOBIC CORE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 89 6428 1992 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : EMBOSS, PRESTO REMARK 3 AUTHORS : NAKAI,KIDERA,NAKAMURA (EMBOSS), MORIKAMI,NAKAI, REMARK 3 KIDERA,SAITO,NAKAMURA (PRESTO) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 A TOTAL OF 50 STRUCTURES WERE CALCULATED. THE COORDINATES REMARK 3 OF THE RESTRAINED MINIMIZED AVERAGED STRUCTURE WERE REMARK 3 OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL REMARK 3 STRUCTURES, AND THEN BY SUBJECTING THE RESULTING REMARK 3 COORDINATES TO THE RESTRAINED ENERGY MINIMIZATION BY REMARK 3 PRESTO. REMARK 4 REMARK 4 1MBK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290; 300 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 50 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: 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 144 -43.53 -163.84 REMARK 500 1 ASN A 164 42.46 -79.82 REMARK 500 1 PRO A 174 -93.51 -70.09 REMARK 500 1 SER A 187 -53.29 -173.83 REMARK 500 2 LYS A 143 -142.04 40.43 REMARK 500 2 LYS A 144 -170.23 63.18 REMARK 500 2 THR A 145 -42.72 -152.49 REMARK 500 2 SER A 146 113.51 77.02 REMARK 500 2 TRP A 147 -174.08 60.13 REMARK 500 2 LEU A 162 -63.39 -97.07 REMARK 500 2 MET A 189 -149.08 -100.15 REMARK 500 2 ARG A 190 -53.26 177.57 REMARK 500 3 LYS A 144 79.95 58.34 REMARK 500 3 MET A 189 -89.48 -82.96 REMARK 500 3 ARG A 190 -55.83 76.91 REMARK 500 4 LYS A 143 -59.74 -154.90 REMARK 500 4 LYS A 144 -171.01 60.61 REMARK 500 4 SER A 146 72.20 -170.76 REMARK 500 4 TRP A 147 169.56 63.33 REMARK 500 4 PRO A 174 -162.31 -62.45 REMARK 500 4 THR A 177 148.77 71.89 REMARK 500 4 ASN A 186 49.05 -79.14 REMARK 500 4 SER A 187 -61.35 -169.03 REMARK 500 4 MET A 189 -104.54 -85.27 REMARK 500 4 ARG A 190 39.91 37.97 REMARK 500 4 ARG A 191 47.79 -148.72 REMARK 500 4 LYS A 192 -61.20 -131.87 REMARK 500 5 THR A 145 52.77 -161.98 REMARK 500 5 SER A 146 44.63 -80.33 REMARK 500 5 TRP A 147 -174.94 56.68 REMARK 500 5 ASN A 164 39.94 -78.10 REMARK 500 5 THR A 188 -72.77 -144.56 REMARK 500 5 MET A 189 38.46 -90.08 REMARK 500 5 LYS A 192 -53.95 73.95 REMARK 500 6 LYS A 144 -67.69 -106.59 REMARK 500 6 THR A 145 27.34 -145.32 REMARK 500 6 TRP A 147 102.96 62.04 REMARK 500 6 ARG A 176 -50.84 -138.09 REMARK 500 6 THR A 177 169.90 65.94 REMARK 500 6 SER A 187 -56.86 -173.02 REMARK 500 6 MET A 189 53.49 -118.28 REMARK 500 7 ASN A 164 34.23 -83.35 REMARK 500 7 MET A 189 52.53 -102.43 REMARK 500 7 ARG A 191 -75.06 68.18 REMARK 500 7 LYS A 192 76.12 49.99 REMARK 500 8 ASN A 164 30.58 -83.08 REMARK 500 8 THR A 177 154.92 68.77 REMARK 500 8 MET A 189 -118.67 -91.54 REMARK 500 8 ARG A 191 -118.17 -131.22 REMARK 500 9 LYS A 143 -70.75 66.13 REMARK 500 REMARK 500 THIS ENTRY HAS 315 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 11 ARG A 153 0.08 SIDE CHAIN REMARK 500 17 ARG A 153 0.08 SIDE CHAIN REMARK 500 23 ARG A 153 0.09 SIDE CHAIN REMARK 500 33 ARG A 165 0.09 SIDE CHAIN REMARK 500 37 ARG A 176 0.08 SIDE CHAIN REMARK 500 49 ARG A 153 0.09 SIDE CHAIN REMARK 500 49 ARG A 165 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 194 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MBJ RELATED DB: PDB DBREF 1MBK A 142 193 UNP P06876 MYB_MOUSE 142 193 SEQRES 1 A 53 VAL LYS LYS THR SER TRP THR GLU GLU GLU ASP ARG ILE SEQRES 2 A 53 ILE TYR GLN ALA HIS LYS ARG LEU GLY ASN ARG TRP ALA SEQRES 3 A 53 GLU ILE ALA LYS LEU LEU PRO GLY ARG THR ASP ASN ALA SEQRES 4 A 53 ILE LYS ASN HIS TRP ASN SER THR MET ARG ARG LYS VAL SEQRES 5 A 53 NH2 HET NH2 A 194 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 H1 GLU A 149 LEU A 162 1 14 HELIX 2 H2 TRP A 166 LEU A 172 1 7 HELIX 3 H3 ASP A 178 SER A 187 1 10 LINK C VAL A 193 N NH2 A 194 1555 1555 1.34 SITE 1 AC1 3 ARG A 191 LYS A 192 VAL A 193 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