PDB Short entry for 1A0A HEADER TRANSCRIPTION/DNA 27-NOV-97 1A0A TITLE PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3'); COMPND 4 CHAIN: C; COMPND 5 FRAGMENT: UPSTREAM ACTIVATION SITE P2; COMPND 6 SYNONYM: UASP2(17); COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'- COMPND 10 D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3'); COMPND 11 CHAIN: D; COMPND 12 FRAGMENT: UPSTREAM ACTIVATION SITE P2; COMPND 13 SYNONYM: UASP2(17); COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN COMPND 17 PHO4); COMPND 18 CHAIN: A, B; COMPND 19 FRAGMENT: DNA BINDING DOMAIN; COMPND 20 SYNONYM: BHLH; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 8 ORGANISM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) KEYWDS TRANSCRIPTION FACTOR, BASIC HELIX LOOP HELIX, COMPLEX (TRANSCRIPTION KEYWDS 2 FACTOR-DNA), TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.SHIMIZU,A.TOUMOTO,K.IHARA,M.SHIMIZU,Y.KYOGOKU,N.OGAWA,Y.OSHIMA, AUTHOR 2 T.HAKOSHIMA REVDAT 3 07-FEB-24 1A0A 1 SEQADV REVDAT 2 24-FEB-09 1A0A 1 VERSN REVDAT 1 18-MAR-98 1A0A 0 JRNL AUTH T.SHIMIZU,A.TOUMOTO,K.IHARA,M.SHIMIZU,Y.KYOGOKU,N.OGAWA, JRNL AUTH 2 Y.OSHIMA,T.HAKOSHIMA JRNL TITL CRYSTAL STRUCTURE OF PHO4 BHLH DOMAIN-DNA COMPLEX: FLANKING JRNL TITL 2 BASE RECOGNITION. JRNL REF EMBO J. V. 16 4689 1997 JRNL REFN ISSN 0261-4189 JRNL PMID 9303313 JRNL DOI 10.1093/EMBOJ/16.15.4689 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 77.3 REMARK 3 NUMBER OF REFLECTIONS : 7581 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) : 0.230 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.500 REMARK 3 FREE R VALUE TEST SET COUNT : 948 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 54.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 569 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 13.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 86 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 996 REMARK 3 NUCLEIC ACID ATOMS : 691 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56000 REMARK 3 B22 (A**2) : 3.90000 REMARK 3 B33 (A**2) : -3.34000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 2.420 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM_NDBX.DNAE REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOP_NDBX.DNA REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A0A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000170232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 288.00 REMARK 200 PH : 3.6 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9398 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.20200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION METHOD: DROP-0.4MM REMARK 280 PROTEIN, 0.2MM DNA, 1% PEG6K, 20MM NACITRATE (PH3.6), RESERVOIR- REMARK 280 1% PEG6K, 20MM NACITRATE(PH3.6), VAPOR DIFFUSION 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 26.75500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.38500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.38500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.75500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.15000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG C 12 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG D 4 N9 - C1' - C2' ANGL. DEV. = -17.0 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT D 5 N1 - C1' - C2' ANGL. DEV. = -19.1 DEGREES REMARK 500 DT D 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES 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 LYS A 1 25.90 -71.23 REMARK 500 ARG A 2 31.12 -60.57 REMARK 500 GLU A 3 -54.69 -164.97 REMARK 500 LYS A 6 -78.17 7.81 REMARK 500 GLU A 9 -80.42 -73.15 REMARK 500 LYS A 32 -34.58 -17.07 REMARK 500 ALA A 39 150.94 150.62 REMARK 500 LYS A 42 41.90 -76.79 REMARK 500 ALA A 43 -53.53 -169.31 REMARK 500 HIS A 55 -72.09 -71.63 REMARK 500 LEU A 56 -30.43 -29.48 REMARK 500 GLN A 57 -77.21 -52.93 REMARK 500 LYS B 1 10.47 -51.56 REMARK 500 HIS B 5 -25.15 -38.77 REMARK 500 LYS B 6 -74.16 -78.05 REMARK 500 HIS B 7 -34.75 -39.80 REMARK 500 ALA B 8 -73.47 -80.25 REMARK 500 GLU B 9 9.39 -55.07 REMARK 500 LEU B 16 -19.47 -46.55 REMARK 500 ALA B 17 -64.82 -93.87 REMARK 500 ALA B 19 -71.36 -64.19 REMARK 500 LEU B 20 -35.70 -39.50 REMARK 500 GLU B 22 20.96 -67.44 REMARK 500 LEU B 23 -68.91 -103.33 REMARK 500 SER B 25 -26.98 -39.71 REMARK 500 LEU B 26 31.89 -154.05 REMARK 500 ALA B 29 88.93 -60.32 REMARK 500 ASN B 35 -178.70 -175.00 REMARK 500 VAL B 36 -17.82 -33.06 REMARK 500 SER B 37 98.16 -20.18 REMARK 500 ALA B 39 120.19 172.13 REMARK 500 SER B 41 -60.68 -169.62 REMARK 500 LYS B 42 -122.08 -125.77 REMARK 500 ALA B 43 -73.61 -1.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A0A A 0 62 UNP P07270 PHO4_YEAST 250 312 DBREF 1A0A B 0 62 UNP P07270 PHO4_YEAST 250 312 DBREF 1A0A C 1 17 PDB 1A0A 1A0A 1 17 DBREF 1A0A D 1 17 PDB 1A0A 1A0A 1 17 SEQADV 1A0A MET A 0 UNP P07270 ASP 250 CONFLICT SEQADV 1A0A ALA A 19 UNP P07270 PRO 269 CONFLICT SEQADV 1A0A MET B 0 UNP P07270 ASP 250 CONFLICT SEQADV 1A0A ALA B 19 UNP P07270 PRO 269 CONFLICT SEQRES 1 C 17 DC DT DC DA DC DA DC DG DT DG DG DG DA SEQRES 2 C 17 DC DT DA DG SEQRES 1 D 17 DC DT DA DG DT DC DC DC DA DC DG DT DG SEQRES 2 D 17 DT DG DA DG SEQRES 1 A 63 MET LYS ARG GLU SER HIS LYS HIS ALA GLU GLN ALA ARG SEQRES 2 A 63 ARG ASN ARG LEU ALA VAL ALA LEU HIS GLU LEU ALA SER SEQRES 3 A 63 LEU ILE PRO ALA GLU TRP LYS GLN GLN ASN VAL SER ALA SEQRES 4 A 63 ALA PRO SER LYS ALA THR THR VAL GLU ALA ALA CYS ARG SEQRES 5 A 63 TYR ILE ARG HIS LEU GLN GLN ASN GLY SER THR SEQRES 1 B 63 MET LYS ARG GLU SER HIS LYS HIS ALA GLU GLN ALA ARG SEQRES 2 B 63 ARG ASN ARG LEU ALA VAL ALA LEU HIS GLU LEU ALA SER SEQRES 3 B 63 LEU ILE PRO ALA GLU TRP LYS GLN GLN ASN VAL SER ALA SEQRES 4 B 63 ALA PRO SER LYS ALA THR THR VAL GLU ALA ALA CYS ARG SEQRES 5 B 63 TYR ILE ARG HIS LEU GLN GLN ASN GLY SER THR FORMUL 5 HOH *80(H2 O) HELIX 1 H1A GLU A 3 ALA A 8 5 6 HELIX 2 H11 GLU A 9 LEU A 26 1 18 HELIX 3 HA PRO A 28 GLN A 33 1 6 HELIX 4 H2A ALA A 43 GLN A 57 1 15 HELIX 5 H1B LYS B 1 LEU B 26 5 26 HELIX 6 HB ALA B 29 GLN B 33 5 5 HELIX 7 H2B LYS B 42 GLN B 57 1 16 CRYST1 53.510 68.300 108.770 90.00 90.00 90.00 P 21 21 21 8 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 0.018688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009194 0.00000