HEADER TRANSCRIPTION 30-JAN-02 1GUU TITLE CRYSTAL STRUCTURE OF C-MYB R1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYB PROTO-ONCOGENE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: R1, RESIDUES 38-89; COMPND 5 SYNONYM: C-MYB; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 4 ORGANISM_COMMON: MOUSE; SOURCE 5 ORGANISM_TAXID: 10090 KEYWDS TRANSCRIPTION, TRANSCRIPTION REGULATION, MYB, C-MYB, DNA BINDING, ION KEYWDS 2 BINDI PROTO-ONCOGENE, NUCLEAR PROTEIN, ACTIVATOR EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,K.OGATA REVDAT 3 13-DEC-23 1GUU 1 LINK REVDAT 2 24-FEB-09 1GUU 1 VERSN REVDAT 1 26-JUN-03 1GUU 0 JRNL AUTH T.H.TAHIROV,H.MORII,H.UEDAIRA,M.SASAKI,A.SARAI,S.ADACHI, JRNL AUTH 2 S.Y.PARK,N.KAMIYA,K.OGATA JRNL TITL CRYSTAL STRUCTURE OF C-MYB DNA-BINDING DOMAIN: SPECIFIC NA+ JRNL TITL 2 BINDING AND CORRELATION WITH NMR STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.H.TAHIROV,K.SATO,E.ICHIKAWA-IWATA,M.SASAKI,T.INOUE-BUNGO, REMARK 1 AUTH 2 M.SHIINA,K.KIMURA,S.TAKATA,A.FUJIKAWA,H.MORII,T.KUMASAKA, REMARK 1 AUTH 3 M.YAMAMOTO,S.ISHII,K.OGATA REMARK 1 TITL MECHANISM OF C-MYB-C/EBPBETA COOPERATION FROM SEPARATED REMARK 1 TITL 2 SITES ON A PROMOTER REMARK 1 REF CELL (CAMBRIDGE,MASS.) V. 108 57 2002 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 11792321 REMARK 1 DOI 10.1016/S0092-8674(01)00636-5 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 729344.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 5531 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 306 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 724 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 35 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.047 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 433 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.44000 REMARK 3 B22 (A**2) : -4.79000 REMARK 3 B33 (A**2) : -1.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.84000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.620 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.840 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.230 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.980 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 50.55 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GUU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1290009371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5574 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 2.959 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6530 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.43 REMARK 200 R MERGE FOR SHELL (I) : 0.20400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.279 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1MBE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6-1.7 M SODIUM CITRATE PH 6.8, REMARK 280 PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS TRANSFORMED TO LOW REMARK 280 HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED REMARK 280 TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING, PH 6.80 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 17.65150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A 38 REMARK 465 GLY A 39 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 88 106.88 -46.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1090 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 67 O REMARK 620 2 LEU A 70 O 89.0 REMARK 620 3 ARG A 73 O 99.0 88.3 REMARK 620 4 HOH A2023 O 89.0 176.0 88.6 REMARK 620 5 HOH A2027 O 166.8 99.6 91.4 83.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1090 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GV2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-MYB R2R3 REMARK 900 RELATED ID: 1GV5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-MYB R2 REMARK 900 RELATED ID: 1H88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 REMARK 900 RELATED ID: 1H89 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 REMARK 900 RELATED ID: 1IDY RELATED DB: PDB REMARK 900 STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZEDAVERAGE REMARK 900 STRUCTURE REMARK 900 RELATED ID: 1IDZ RELATED DB: PDB REMARK 900 STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, 20 STRUCTURES REMARK 900 RELATED ID: 1MBE RELATED DB: PDB REMARK 900 MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 1 REMARK 900 RELATED ID: 1MBF RELATED DB: PDB REMARK 900 MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 1 REMARK 900 RELATED ID: 1MBG RELATED DB: PDB REMARK 900 MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 2 REMARK 900 RELATED ID: 1MBH RELATED DB: PDB REMARK 900 MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 2 REMARK 900 RELATED ID: 1MBJ RELATED DB: PDB REMARK 900 MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 3 REMARK 900 RELATED ID: 1MBK RELATED DB: PDB REMARK 900 MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 3 REMARK 900 RELATED ID: 1MSE RELATED DB: PDB REMARK 900 C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN COMPLEXED WITH REMARK 900 DEOXYRIBONUCLEIC ACID (NMR, MINIMIZED AVERAGE STRUCTURE) REMARK 900 RELATED ID: 1MSF RELATED DB: PDB REMARK 900 C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN COMPLEXED WITH REMARK 900 DEOXYRIBONUCLEIC ACID (NMR, 25 STRUCTURES) DBREF 1GUU A 38 89 UNP P06876 MYB_MOUSE 38 89 SEQRES 1 A 52 LEU GLY LYS THR ARG TRP THR ARG GLU GLU ASP GLU LYS SEQRES 2 A 52 LEU LYS LYS LEU VAL GLU GLN ASN GLY THR ASP ASP TRP SEQRES 3 A 52 LYS VAL ILE ALA ASN TYR LEU PRO ASN ARG THR ASP VAL SEQRES 4 A 52 GLN CYS GLN HIS ARG TRP GLN LYS VAL LEU ASN PRO GLU HET NA A1090 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *42(H2 O) HELIX 1 1 THR A 44 GLY A 59 1 16 HELIX 2 2 ASP A 62 TYR A 69 1 8 HELIX 3 3 THR A 74 ASN A 87 1 14 LINK O ALA A 67 NA NA A1090 1555 1555 2.31 LINK O LEU A 70 NA NA A1090 1555 1555 2.46 LINK O ARG A 73 NA NA A1090 1555 1555 2.54 LINK NA NA A1090 O HOH A2023 1555 1555 2.55 LINK NA NA A1090 O HOH A2027 1555 1555 2.41 SITE 1 AC1 5 ALA A 67 LEU A 70 ARG A 73 HOH A2023 SITE 2 AC1 5 HOH A2027 CRYST1 26.273 35.303 24.039 90.00 93.37 90.00 P 1 21 1 2 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 0.038062 0.000000 0.002241 0.00000 SCALE2 0.000000 0.028326 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041671 0.00000