HEADER DNA BINDING PROTEIN 11-MAY-20 6Z0S TITLE ALLOSTERY THROUGH DNA DRIVES PHENOTYPE SWITCHING COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMG PROMOTER DNA - STRAND A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 84-MER MODELED UPON 93 NUCLEOTIDES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COMG PROMOTER DNA - STRAND B; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: 86-MER MODELED UPON 93 NUCLEOTIDES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 4 ORGANISM_TAXID: 1423; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 8 ORGANISM_TAXID: 1423 KEYWDS TRANSCRIPTION-FACTOR, DNA-BINDING, A-TRACT, ALLOSTERY, DNA BINDING KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR G.ROSENBLUM,N.ELAD,H.ROZENBERG,F.WIGGERS,J.JUNGWIRTH,H.HOFMANN REVDAT 2 02-JUN-21 6Z0S 1 JRNL REVDAT 1 07-APR-21 6Z0S 0 JRNL AUTH G.ROSENBLUM,N.ELAD,H.ROZENBERG,F.WIGGERS,J.JUNGWIRTH, JRNL AUTH 2 H.HOFMANN JRNL TITL ALLOSTERY THROUGH DNA DRIVES PHENOTYPE SWITCHING. JRNL REF NAT COMMUN V. 12 2967 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34016970 JRNL DOI 10.1038/S41467-021-23148-2 REMARK 2 REMARK 2 RESOLUTION. 5.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, CRYOSPARC, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 5.700 REMARK 3 NUMBER OF PARTICLES : 88140 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6Z0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108605. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : COMK TRANSCRIPTION FACTOR BOUND REMARK 245 TO ITS COMG PROMOTER DNA. REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.24 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5570.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : 58207 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 7530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 DC A 1 REMARK 465 DA A 2 REMARK 465 DG A 3 REMARK 465 DT A 4 REMARK 465 DT A 5 REMARK 465 DG A 6 REMARK 465 DA A 7 REMARK 465 DA A 8 REMARK 465 DA A 9 REMARK 465 DT B 85 REMARK 465 DT B 86 REMARK 465 DT B 87 REMARK 465 DC B 88 REMARK 465 DA B 89 REMARK 465 DA B 90 REMARK 465 DC B 91 REMARK 465 DT B 92 REMARK 465 DG B 93 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 DT A 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 46 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA A 46 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC A 67 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 63 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT B 69 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-11022 RELATED DB: EMDB REMARK 900 ALLOSTERY THROUGH DNA DRIVES PHENOTYPE SWITCHING REMARK 900 RELATED ID: EMD-12260 RELATED DB: EMDB DBREF 6Z0S A 1 93 PDB 6Z0S 6Z0S 1 93 DBREF 6Z0S B 1 93 PDB 6Z0S 6Z0S 1 93 SEQRES 1 A 93 DC DA DG DT DT DG DA DA DA DG DT DC DT SEQRES 2 A 93 DT DT DT DT DT DC DT DT DG DC DC DA DG SEQRES 3 A 93 DA DA DA DG DA DA DT DT DG DG DT DT DT SEQRES 4 A 93 DT DT DC DA DG DC DA DT DA DT DA DA DC SEQRES 5 A 93 DA DT DC DT DC DA DC DA DA DA DA DT DC SEQRES 6 A 93 DA DC DG DT DT DT DT DC DC DC DT DG DT SEQRES 7 A 93 DT DT DG DA DT DT DA DC DC DT DT DT DT SEQRES 8 A 93 DC DT SEQRES 1 B 93 DA DG DA DA DA DA DG DG DT DA DA DT DC SEQRES 2 B 93 DA DA DA DC DA DG DG DG DA DA DA DA DC SEQRES 3 B 93 DG DT DG DA DT DT DT DT DG DT DG DA DG SEQRES 4 B 93 DA DT DG DT DT DA DT DA DT DG DC DT DG SEQRES 5 B 93 DA DA DA DA DA DC DC DA DA DT DT DC DT SEQRES 6 B 93 DT DT DC DT DG DG DC DA DA DG DA DA DA SEQRES 7 B 93 DA DA DA DG DA DC DT DT DT DC DA DA DC SEQRES 8 B 93 DT DG CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000