HEADER DNA BINDING PROTEIN 01-MAY-25 9R2Z TITLE RPTR TRANSCRIPTIONAL REPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRANSCRIPTION FACTOR; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O127:H6 STR. E2348/69; SOURCE 3 ORGANISM_TAXID: 574521; SOURCE 4 GENE: E2348C_1096; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O127:H6 STR. E2348/69; SOURCE 9 ORGANISM_TAXID: 574521; SOURCE 10 GENE: E2348C_1096; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRANSCRIPTIONAL REGULATOR, DNA BINDING, REPRESSOR, HELICAL, DNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,M.SCHULLER,I.AHEL,T.R.BLOWER,R.M.EXLEY,C.M.TANG REVDAT 1 23-JUL-25 9R2Z 0 JRNL AUTH Y.ZHANG,M.SCHULLER,I.AHEL,T.R.BLOWER,R.M.EXLEY,C.M.TANG JRNL TITL REGULATION OF A PHAGE DEFENCE ISLAND BY RPTR, A NOVEL JRNL TITL 2 REPRESSOR THAT CONTROLS RESTRICTION-MODIFICATION SYSTEMS IN JRNL TITL 3 DIVERSE BACTERIA. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40650974 JRNL DOI 10.1093/NAR/GKAF645 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 39026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1875 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 34.7200 - 3.0600 1.00 2937 158 0.1620 0.1936 REMARK 3 2 3.0600 - 2.4300 1.00 2918 137 0.1678 0.1924 REMARK 3 3 2.4300 - 2.1200 1.00 2900 143 0.1589 0.1675 REMARK 3 4 2.1200 - 1.9300 1.00 2876 131 0.1515 0.2090 REMARK 3 5 1.9300 - 1.7900 1.00 2814 200 0.1580 0.1774 REMARK 3 6 1.7900 - 1.6800 1.00 2874 124 0.1622 0.2190 REMARK 3 7 1.6800 - 1.6000 1.00 2824 156 0.1542 0.1921 REMARK 3 8 1.6000 - 1.5300 0.99 2818 156 0.1603 0.1817 REMARK 3 9 1.5300 - 1.4700 0.99 2843 137 0.1679 0.1929 REMARK 3 10 1.4700 - 1.4200 0.99 2871 144 0.1849 0.2437 REMARK 3 11 1.4200 - 1.3700 0.99 2808 145 0.1969 0.2318 REMARK 3 12 1.3700 - 1.3400 0.99 2833 114 0.2045 0.2431 REMARK 3 13 1.3400 - 1.3000 0.98 2835 130 0.2267 0.2517 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.129 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.59 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 : 0.005 1272 REMARK 3 ANGLE : 0.791 1706 REMARK 3 CHIRALITY : 0.062 193 REMARK 3 PLANARITY : 0.005 219 REMARK 3 DIHEDRAL : 4.503 173 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9R2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1292147408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-25 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51246 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 REMARK 200 RESOLUTION RANGE LOW (A) : 34.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 MM POTASSIUM THIOCYANATE, 32% PEG REMARK 280 2000 MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 20.77050 REMARK 290 SMTRY3 2 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: 1680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET A 1 N CA CB CG 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 OE2 GLU A 5 O HOH A 101 1.81 REMARK 500 O HOH B 138 O HOH B 160 2.00 REMARK 500 O HOH A 201 O HOH A 210 2.02 REMARK 500 O HOH A 116 O HOH A 135 2.04 REMARK 500 O HOH B 125 O HOH B 126 2.06 REMARK 500 O HOH A 107 O HOH A 182 2.07 REMARK 500 O HOH B 105 O HOH B 167 2.08 REMARK 500 NE2 GLN A 21 O HOH A 102 2.09 REMARK 500 OD1 ASP A 2 O HOH A 103 2.10 REMARK 500 O HOH A 108 O HOH A 166 2.18 REMARK 500 O HOH B 146 O HOH A 188 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 171 O HOH A 194 1565 2.09 REMARK 500 O HOH B 115 O HOH B 160 2546 2.10 REMARK 500 O HOH A 176 O HOH A 204 1455 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 213 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 214 DISTANCE = 6.43 ANGSTROMS DBREF 9R2Z B 2 79 UNP B7UP23 B7UP23_ECO27 2 79 DBREF 9R2Z A 1 79 UNP B7UP23 B7UP23_ECO27 1 79 SEQRES 1 B 78 ASP GLU ASP GLU ILE TYR ARG HIS ILE ARG GLN ALA LEU SEQRES 2 B 78 SER SER ALA PRO ARG ASN GLN TYR THR VAL GLU LEU HIS SEQRES 3 B 78 LEU GLN MET ILE LYS TYR ALA ASP LYS LEU GLU HIS ILE SEQRES 4 B 78 THR ALA LYS ALA PHE CYS GLU GLY THR GLY LEU SER GLN SEQRES 5 B 78 SER LEU GLY THR GLU PHE SER LYS MET ARG ASN LEU THR SEQRES 6 B 78 ARG ARG LEU LYS ALA ALA GLY LEU ASN THR ASP LEU LEU SEQRES 1 A 79 MET ASP GLU ASP GLU ILE TYR ARG HIS ILE ARG GLN ALA SEQRES 2 A 79 LEU SER SER ALA PRO ARG ASN GLN TYR THR VAL GLU LEU SEQRES 3 A 79 HIS LEU GLN MET ILE LYS TYR ALA ASP LYS LEU GLU HIS SEQRES 4 A 79 ILE THR ALA LYS ALA PHE CYS GLU GLY THR GLY LEU SER SEQRES 5 A 79 GLN SER LEU GLY THR GLU PHE SER LYS MET ARG ASN LEU SEQRES 6 A 79 THR ARG ARG LEU LYS ALA ALA GLY LEU ASN THR ASP LEU SEQRES 7 A 79 LEU FORMUL 3 HOH *194(H2 O) HELIX 1 AA1 ASP B 2 SER B 16 1 15 HELIX 2 AA2 PRO B 18 ASN B 20 5 3 HELIX 3 AA3 GLN B 21 ALA B 34 1 14 HELIX 4 AA4 ASP B 35 LEU B 37 5 3 HELIX 5 AA5 THR B 41 GLY B 50 1 10 HELIX 6 AA6 SER B 52 SER B 54 5 3 HELIX 7 AA7 LEU B 55 ALA B 72 1 18 HELIX 8 AA8 ASN B 75 LEU B 79 5 5 HELIX 9 AA9 ASP A 2 ALA A 17 1 16 HELIX 10 AB1 PRO A 18 ASN A 20 5 3 HELIX 11 AB2 GLN A 21 ALA A 34 1 14 HELIX 12 AB3 ASP A 35 LEU A 37 5 3 HELIX 13 AB4 THR A 41 GLY A 50 1 10 HELIX 14 AB5 SER A 52 SER A 54 5 3 HELIX 15 AB6 LEU A 55 ASN A 64 1 10 HELIX 16 AB7 LEU A 65 ALA A 72 1 8 HELIX 17 AB8 ASN A 75 LEU A 79 5 5 CRYST1 30.603 41.541 63.261 90.00 90.12 90.00 P 1 21 1 2 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 0.032677 0.000000 0.000066 0.00000 SCALE2 0.000000 0.024073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015808 0.00000 MASTER 259 0 0 17 0 0 0 6 1450 2 0 13 END