PDB Short entry for 1GV5 HEADER TRANSCRIPTION 06-FEB-02 1GV5 TITLE CRYSTAL STRUCTURE OF C-MYB R2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYB PROTO-ONCOGENE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: R2, RESIDUES 90-141; COMPND 5 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 EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,K.OGATA REVDAT 4 13-DEC-23 1GV5 1 LINK REVDAT 3 08-MAY-19 1GV5 1 REMARK REVDAT 2 24-FEB-09 1GV5 1 VERSN REVDAT 1 03-JUL-03 1GV5 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 1 REFERENCE 2 REMARK 1 AUTH T.H.TAHIROV,H.MORII,H.UEDAIRA,A.SARAI,K.OGATA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF WILD TYPE REMARK 1 TITL 2 AND V103L MUTANT MYB R2 DNA-BINDING DOMAIN REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 1345 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10393303 REMARK 1 DOI 10.1107/S0907444999005041 REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 408120.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 8174 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) : 0.178 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 446 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1206 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 61 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 445 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.52000 REMARK 3 B22 (A**2) : -2.70000 REMARK 3 B33 (A**2) : 1.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.08 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 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) : 2.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.660 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.580 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.57 REMARK 3 BSOL : 90.09 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 1GV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1290009410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MAC SCIENCE M06XHF22 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : 0.15 MM NICKEL FILTER REMARK 200 OPTICS : MAC SCIENCE DOUBLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8207 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.16 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.7360 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.17 REMARK 200 R MERGE FOR SHELL (I) : 0.32900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.285 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 1MBG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.65 M SODIUM CITRATE PH 6.8, PROTEIN REMARK 280 CONCENTRATION 10 MG/ML PLUS 10 MM DTT, TEMPERATURE 297 K, PH 6.80 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 14.41600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.61450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.09100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.61450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.41600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.09100 REMARK 290 SMTRY3 4 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 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 112 60.16 -68.88 REMARK 500 LYS A 113 -164.69 -166.39 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 A1142 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 119 O REMARK 620 2 LEU A 122 O 82.7 REMARK 620 3 ARG A 125 O 100.6 94.5 REMARK 620 4 HOH A2024 O 88.0 170.2 90.4 REMARK 620 5 HOH A2025 O 95.5 86.5 163.9 91.3 REMARK 620 6 HOH A2029 O 172.9 99.8 85.9 89.0 78.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1142 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GUU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-MYB R1 REMARK 900 RELATED ID: 1GV2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-MYB R2R3 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 1GV5 A 90 141 UNP P06876 MYB_MOUSE 90 141 SEQADV 1GV5 LYS A 105 UNP P06876 GLN 105 VARIANT SEQRES 1 A 52 LEU ILE LYS GLY PRO TRP THR LYS GLU GLU ASP GLN ARG SEQRES 2 A 52 VAL ILE LYS LEU VAL GLN LYS TYR GLY PRO LYS ARG TRP SEQRES 3 A 52 SER VAL ILE ALA LYS HIS LEU LYS GLY ARG ILE GLY LYS SEQRES 4 A 52 GLN CYS ARG GLU ARG TRP HIS ASN HIS LEU ASN PRO GLU HET NA A1142 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *50(H2 O) HELIX 1 1 THR A 96 GLY A 111 1 16 HELIX 2 2 ARG A 114 LYS A 120 1 7 HELIX 3 3 ILE A 126 HIS A 137 1 12 LINK O ALA A 119 NA NA A1142 1555 1555 2.36 LINK O LEU A 122 NA NA A1142 1555 1555 2.40 LINK O ARG A 125 NA NA A1142 1555 1555 2.36 LINK NA NA A1142 O HOH A2024 1555 1555 2.39 LINK NA NA A1142 O HOH A2025 1555 1555 2.48 LINK NA NA A1142 O HOH A2029 1555 1555 2.47 SITE 1 AC1 6 ALA A 119 LEU A 122 ARG A 125 HOH A2024 SITE 2 AC1 6 HOH A2025 HOH A2029 CRYST1 28.832 40.182 49.229 90.00 90.00 90.00 P 21 21 21 4 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 0.034684 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020313 0.00000