HEADER DNA BINDING PROTEIN 12-OCT-25 9X5A TITLE CRYSTAL STRUCTURE OF THE NEGATIVE REGULATOR MIHR2 IN MIHARAMYCIN TITLE 2 BIOSYNTHESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: XRE FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES MIHARAENSIS; SOURCE 3 ORGANISM_TAXID: 285483; SOURCE 4 GENE: MIHR2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NEGATIVE REGULATOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SUN REVDAT 1 28-OCT-26 9X5A 0 JRNL AUTH A.SUN JRNL TITL CRYSTAL STRUCTURE OF THE NEGATIVE REGULATOR MIHR2 IN JRNL TITL 2 MIHARAMYCIN BIOSYNTHESIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.21.2-5419 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 26311 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.540 REMARK 3 FREE R VALUE TEST SET COUNT : 1983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 53.8200 - 5.0700 0.99 1969 162 0.1658 0.2167 REMARK 3 2 5.0700 - 4.0200 1.00 1892 154 0.1559 0.1895 REMARK 3 3 4.0200 - 3.5100 0.88 1633 133 0.1895 0.1966 REMARK 3 4 3.5100 - 3.1900 0.88 1644 123 0.2161 0.2495 REMARK 3 5 3.1900 - 2.9600 1.00 1823 153 0.2357 0.3218 REMARK 3 6 2.9600 - 2.7900 1.00 1858 153 0.2242 0.2921 REMARK 3 7 2.7900 - 2.6500 0.89 1619 125 0.2302 0.3238 REMARK 3 8 2.6500 - 2.5300 1.00 1810 158 0.2165 0.2595 REMARK 3 9 2.5300 - 2.4400 1.00 1828 150 0.2097 0.2509 REMARK 3 10 2.4400 - 2.3500 1.00 1826 149 0.2001 0.2644 REMARK 3 11 2.3500 - 2.2800 1.00 1825 143 0.2100 0.2735 REMARK 3 12 2.2800 - 2.2100 0.54 971 77 0.2919 0.4083 REMARK 3 13 2.2100 - 2.1600 1.00 1835 147 0.2294 0.2750 REMARK 3 14 2.1600 - 2.1000 1.00 1795 156 0.2574 0.3198 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2828 REMARK 3 ANGLE : 0.766 3838 REMARK 3 CHIRALITY : 0.039 449 REMARK 3 PLANARITY : 0.009 509 REMARK 3 DIHEDRAL : 15.259 1044 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 0.6197 -10.0730 -40.7079 REMARK 3 T TENSOR REMARK 3 T11: 0.1924 T22: 0.1577 REMARK 3 T33: 0.1783 T12: -0.0038 REMARK 3 T13: -0.0004 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.1529 L22: -0.0370 REMARK 3 L33: 0.0551 L12: -0.0368 REMARK 3 L13: 0.0406 L23: -0.0371 REMARK 3 S TENSOR REMARK 3 S11: -0.0131 S12: 0.0115 S13: 0.0131 REMARK 3 S21: 0.0138 S22: -0.0133 S23: -0.0037 REMARK 3 S31: -0.0227 S32: -0.0190 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9X5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 16-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1300064283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26505 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 57.426 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M KCL, 0.01 M MGCL2, 0.05 M MES, REMARK 280 PH 6.0, 10 % (V/V) POLYETHYLENE GLYCOL 400, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K 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 35.47000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.30300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.94350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.30300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.47000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.94350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -35.47000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -39.94350 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -82.60600 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 SER B 4 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 47 CB CG CD1 CD2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 ARG A 56 CD NE CZ NH1 NH2 REMARK 470 LYS B 117 CG CD CE NZ REMARK 470 SER B 173 OG REMARK 470 GLU B 177 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 210 O HOH A 259 2.19 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 LEU A 30 -154.67 -106.36 REMARK 500 ARG A 131 76.71 -109.45 REMARK 500 ASP B 91 79.81 -119.16 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9X5A A 4 190 UNP A0A7S5HW86_9ACTN DBREF2 9X5A A A0A7S5HW86 4 190 DBREF1 9X5A B 4 190 UNP A0A7S5HW86_9ACTN DBREF2 9X5A B A0A7S5HW86 4 190 SEQRES 1 A 187 SER SER ASP VAL GLY SER ARG ILE ARG ARG LEU ARG ARG SEQRES 2 A 187 ALA ALA GLY LEU SER GLN ALA ASP LEU ALA GLY GLY GLU SEQRES 3 A 187 LEU SER PRO SER TYR VAL SER LEU LEU GLU ALA GLY LYS SEQRES 4 A 187 ARG THR PRO SER LEU ASP VAL LEU ALA GLN LEU ALA LYS SEQRES 5 A 187 ARG LEU GLY CYS ASP VAL SER GLU LEU THR GLY GLY PRO SEQRES 6 A 187 VAL GLU ALA THR ILE GLY ASP LEU GLU VAL LYS LEU LYS SEQRES 7 A 187 TYR ALA GLU MET ALA LEU ASN ASN GLY ASP PRO HIS ALA SEQRES 8 A 187 ALA LEU GLU ALA TYR ARG SER VAL GLN ASP THR ALA THR SEQRES 9 A 187 PRO ASP ALA GLN PRO GLU ILE TRP TYR LYS ALA GLU HIS SEQRES 10 A 187 GLY VAL ALA ARG ALA LEU GLU HIS ALA GLY ARG LEU GLU SEQRES 11 A 187 GLU ALA VAL ALA HIS LEU GLU GLY LEU ARG SER ALA SER SEQRES 12 A 187 VAL ASP ARG PRO ASP LEU VAL ALA HIS LEU THR VAL VAL SEQRES 13 A 187 ILE ALA LEU CYS ARG CYS TYR ARG GLU LEU GLY ASP LEU SEQRES 14 A 187 SER HIS ALA ILE GLU LEU ALA GLU ALA THR LEU GLU GLU SEQRES 15 A 187 LEU GLN LYS LEU ASN SEQRES 1 B 187 SER SER ASP VAL GLY SER ARG ILE ARG ARG LEU ARG ARG SEQRES 2 B 187 ALA ALA GLY LEU SER GLN ALA ASP LEU ALA GLY GLY GLU SEQRES 3 B 187 LEU SER PRO SER TYR VAL SER LEU LEU GLU ALA GLY LYS SEQRES 4 B 187 ARG THR PRO SER LEU ASP VAL LEU ALA GLN LEU ALA LYS SEQRES 5 B 187 ARG LEU GLY CYS ASP VAL SER GLU LEU THR GLY GLY PRO SEQRES 6 B 187 VAL GLU ALA THR ILE GLY ASP LEU GLU VAL LYS LEU LYS SEQRES 7 B 187 TYR ALA GLU MET ALA LEU ASN ASN GLY ASP PRO HIS ALA SEQRES 8 B 187 ALA LEU GLU ALA TYR ARG SER VAL GLN ASP THR ALA THR SEQRES 9 B 187 PRO ASP ALA GLN PRO GLU ILE TRP TYR LYS ALA GLU HIS SEQRES 10 B 187 GLY VAL ALA ARG ALA LEU GLU HIS ALA GLY ARG LEU GLU SEQRES 11 B 187 GLU ALA VAL ALA HIS LEU GLU GLY LEU ARG SER ALA SER SEQRES 12 B 187 VAL ASP ARG PRO ASP LEU VAL ALA HIS LEU THR VAL VAL SEQRES 13 B 187 ILE ALA LEU CYS ARG CYS TYR ARG GLU LEU GLY ASP LEU SEQRES 14 B 187 SER HIS ALA ILE GLU LEU ALA GLU ALA THR LEU GLU GLU SEQRES 15 B 187 LEU GLN LYS LEU ASN FORMUL 3 HOH *283(H2 O) HELIX 1 AA1 SER A 5 ALA A 18 1 14 HELIX 2 AA2 SER A 21 GLY A 27 1 7 HELIX 3 AA3 SER A 31 ALA A 40 1 10 HELIX 4 AA4 SER A 46 GLY A 58 1 13 HELIX 5 AA5 ASP A 60 THR A 65 1 6 HELIX 6 AA6 VAL A 69 ASN A 89 1 21 HELIX 7 AA7 ASP A 91 ASP A 104 1 14 HELIX 8 AA8 GLN A 111 ALA A 129 1 19 HELIX 9 AA9 ARG A 131 ARG A 149 1 19 HELIX 10 AB1 ALA A 154 LEU A 169 1 16 HELIX 11 AB2 ASP A 171 LYS A 188 1 18 HELIX 12 AB3 ASP B 6 ALA B 18 1 13 HELIX 13 AB4 SER B 21 ALA B 26 1 6 HELIX 14 AB5 SER B 31 ALA B 40 1 10 HELIX 15 AB6 SER B 46 GLY B 58 1 13 HELIX 16 AB7 VAL B 61 GLY B 66 1 6 HELIX 17 AB8 VAL B 69 ASN B 89 1 21 HELIX 18 AB9 ASP B 91 ASP B 104 1 14 HELIX 19 AC1 GLN B 111 ALA B 129 1 19 HELIX 20 AC2 ARG B 131 SER B 144 1 14 HELIX 21 AC3 ARG B 149 VAL B 153 5 5 HELIX 22 AC4 ALA B 154 LEU B 169 1 16 HELIX 23 AC5 ASP B 171 LEU B 189 1 19 CRYST1 70.940 79.887 82.606 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 0.014096 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012106 0.00000 MASTER 275 0 0 23 0 0 0 6 3073 2 0 30 END