HEADER TRANSCRIPTION 27-MAR-04 1SV4 TITLE CRYSTAL STRUCTURE OF YAN-SAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ETS DNA-BINDING PROTEIN POKKURI; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SAM DOMAIN OF TRANSCRIPTION REPRESSOR YAN; COMPND 5 SYNONYM: PROTEIN YAN, PROTEIN ANTERIOR OPEN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: AOP, POK, YAN, CG3166; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET-3C KEYWDS ALPHA-HELIX, 3(10)-HELIX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR F.QIAO,H.SONG,C.A.KIM,M.R.SAWAYA,J.B.HUNTER,M.GINGERY,I.REBAY, AUTHOR 2 A.J.COUREY,J.U.BOWIE REVDAT 4 23-AUG-23 1SV4 1 REMARK REVDAT 3 27-OCT-21 1SV4 1 SEQADV REVDAT 2 24-FEB-09 1SV4 1 VERSN REVDAT 1 27-JUL-04 1SV4 0 JRNL AUTH F.QIAO,H.SONG,C.A.KIM,M.R.SAWAYA,J.B.HUNTER,M.GINGERY, JRNL AUTH 2 I.REBAY,A.J.COUREY,J.U.BOWIE JRNL TITL DEREPRESSION BY DEPOLYMERIZATION; STRUCTURAL INSIGHTS INTO JRNL TITL 2 THE REGULATION OF YAN BY MAE. JRNL REF CELL(CAMBRIDGE,MASS.) V. 118 163 2004 JRNL REFN ISSN 0092-8674 JRNL PMID 15260987 JRNL DOI 10.1016/J.CELL.2004.07.010 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1216458.840 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9986 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) : 0.218 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 529 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1563 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 74 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1277 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.60000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : 5.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.130 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) : 1.550 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.460 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.260 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.460 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 43.28 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SV4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS 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 : 9998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 6.250 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.25 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44300 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1JI7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MPD , PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.25500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.25500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.70500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ARG A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS B 121 REMARK 465 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 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 73 -162.10 -71.95 REMARK 500 CYS A 99 82.18 -157.87 REMARK 500 ALA A 102 33.37 -141.55 REMARK 500 LYS B 74 57.18 -116.07 REMARK 500 CYS B 99 67.44 -151.80 REMARK 500 ALA B 102 35.87 -146.78 REMARK 500 SER B 119 -88.96 -49.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SV0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YAN-SAM/MAE-SAM COMPLEX DBREF 1SV4 A 42 118 UNP Q01842 POK_DROME 42 118 DBREF 1SV4 B 42 118 UNP Q01842 POK_DROME 42 118 SEQADV 1SV4 ARG A 86 UNP Q01842 ALA 86 ENGINEERED MUTATION SEQADV 1SV4 SER A 119 UNP Q01842 CLONING ARTIFACT SEQADV 1SV4 ARG A 120 UNP Q01842 CLONING ARTIFACT SEQADV 1SV4 HIS A 121 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS A 122 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS A 123 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS A 124 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS A 125 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS A 126 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 ARG B 86 UNP Q01842 ALA 86 ENGINEERED MUTATION SEQADV 1SV4 SER B 119 UNP Q01842 CLONING ARTIFACT SEQADV 1SV4 ARG B 120 UNP Q01842 CLONING ARTIFACT SEQADV 1SV4 HIS B 121 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS B 122 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS B 123 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS B 124 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS B 125 UNP Q01842 EXPRESSION TAG SEQADV 1SV4 HIS B 126 UNP Q01842 EXPRESSION TAG SEQRES 1 A 85 GLN LEU PRO PRO SER LEU PRO SER ASP PRO ARG LEU TRP SEQRES 2 A 85 SER ARG GLU ASP VAL LEU VAL PHE LEU ARG PHE CYS VAL SEQRES 3 A 85 ARG GLU PHE ASP LEU PRO LYS LEU ASP PHE ASP LEU PHE SEQRES 4 A 85 GLN MET ASN GLY LYS ARG LEU CYS LEU LEU THR ARG ALA SEQRES 5 A 85 ASP PHE GLY HIS ARG CYS PRO GLY ALA GLY ASP VAL LEU SEQRES 6 A 85 HIS ASN VAL LEU GLN MET LEU ILE ILE GLU SER HIS SER SEQRES 7 A 85 ARG HIS HIS HIS HIS HIS HIS SEQRES 1 B 85 GLN LEU PRO PRO SER LEU PRO SER ASP PRO ARG LEU TRP SEQRES 2 B 85 SER ARG GLU ASP VAL LEU VAL PHE LEU ARG PHE CYS VAL SEQRES 3 B 85 ARG GLU PHE ASP LEU PRO LYS LEU ASP PHE ASP LEU PHE SEQRES 4 B 85 GLN MET ASN GLY LYS ARG LEU CYS LEU LEU THR ARG ALA SEQRES 5 B 85 ASP PHE GLY HIS ARG CYS PRO GLY ALA GLY ASP VAL LEU SEQRES 6 B 85 HIS ASN VAL LEU GLN MET LEU ILE ILE GLU SER HIS SER SEQRES 7 B 85 ARG HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *69(H2 O) HELIX 1 1 ASP A 50 TRP A 54 5 5 HELIX 2 2 SER A 55 PHE A 70 1 16 HELIX 3 3 ASP A 76 GLN A 81 5 6 HELIX 4 4 ASN A 83 CYS A 88 1 6 HELIX 5 5 THR A 91 CYS A 99 1 9 HELIX 6 6 ALA A 102 SER A 119 1 18 HELIX 7 7 ASP B 50 TRP B 54 5 5 HELIX 8 8 SER B 55 PHE B 70 1 16 HELIX 9 9 ASP B 76 GLN B 81 5 6 HELIX 10 10 ASN B 83 CYS B 88 1 6 HELIX 11 11 THR B 91 CYS B 99 1 9 HELIX 12 12 ALA B 102 ARG B 120 1 19 CRYST1 76.510 45.410 55.600 90.00 108.47 90.00 C 1 2 1 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 0.013070 0.000000 0.004366 0.00000 SCALE2 0.000000 0.022022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018962 0.00000