HEADER DNA BINDING PROTEIN 30-JAN-22 7QZ6 TITLE TRANSCRIPTIONAL REGULATOR LMRR WITH BOUND DAUNOMYCIN AND WITH TRP-67 TITLE 2 AND TRP-96 REPLACED BY 5-FLUOROTRP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS CREMORIS; SOURCE 3 ORGANISM_TAXID: 1359; SOURCE 4 STRAIN: MG1363; SOURCE 5 GENE: LLMG_0323; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTIONAL REGULATOR, PADR, FLUORINATED TRYPTOPHAN, DAUNOMYCIN, KEYWDS 2 PI-PI INTERACTIONS, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.W.H.THUNNISSEN REVDAT 2 31-JAN-24 7QZ6 1 REMARK REVDAT 1 23-NOV-22 7QZ6 0 JRNL AUTH J.SHAO,B.P.KUIPER,A.W.H.THUNNISSEN,R.H.COOL,L.ZHOU,C.HUANG, JRNL AUTH 2 B.W.DIJKSTRA,J.BROOS JRNL TITL THE ROLE OF TRYPTOPHAN IN PI INTERACTIONS IN PROTEINS: AN JRNL TITL 2 EXPERIMENTAL APPROACH. JRNL REF J.AM.CHEM.SOC. V. 144 13815 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 35868012 JRNL DOI 10.1021/JACS.2C04986 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1-4487 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 13442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 696 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 43.4700 - 3.6800 0.99 2622 153 0.1838 0.2657 REMARK 3 2 3.6800 - 2.9200 0.99 2530 145 0.2522 0.2712 REMARK 3 3 2.9200 - 2.5500 1.00 2560 114 0.2939 0.3557 REMARK 3 4 2.5500 - 2.3200 0.99 2504 145 0.2927 0.3319 REMARK 3 5 2.3200 - 2.1500 1.00 2530 139 0.3495 0.3955 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.09 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 5 THROUGH 68 OR RESID REMARK 3 74 THROUGH 112)) REMARK 3 SELECTION : (CHAIN B AND (RESID 5 THROUGH 68 OR RESID REMARK 3 74 THROUGH 112)) REMARK 3 ATOM PAIRS NUMBER : 1018 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7QZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1292120661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976250 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13450 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 43.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 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) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.63800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3F8B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 6 MG/ML IN 20 MM REMARK 280 TRIS-HCL, PH 8.0, 300 MM NACL. RESERVOIR SOLUTION: 100 MM HEPES, REMARK 280 PH 7.0, 200 MM NH4CL, 20% PEG 6000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K 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 51.57850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.69100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.57850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.69100 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: 3740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 ILE A 4 REMARK 465 ASP A 69 REMARK 465 GLU A 70 REMARK 465 SER A 71 REMARK 465 GLN A 72 REMARK 465 GLU A 113 REMARK 465 ALA A 114 REMARK 465 ILE A 115 REMARK 465 LYS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 ILE B 4 REMARK 465 GLU B 70 REMARK 465 SER B 71 REMARK 465 GLN B 72 REMARK 465 GLY B 73 REMARK 465 GLU B 113 REMARK 465 ALA B 114 REMARK 465 ILE B 115 REMARK 465 LYS B 116 REMARK 465 HIS B 117 REMARK 465 HIS B 118 REMARK 465 HIS B 119 REMARK 465 HIS B 120 REMARK 465 HIS B 121 REMARK 465 HIS B 122 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 ASN A 40 46.63 36.94 REMARK 500 ASN B 40 48.16 39.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7QZ5 RELATED DB: PDB REMARK 900 RELATED ID: 7QZ7 RELATED DB: PDB REMARK 900 RELATED ID: 7QZ8 RELATED DB: PDB REMARK 900 RELATED ID: 7QZ9 RELATED DB: PDB DBREF 7QZ6 A 1 116 UNP A2RI36 A2RI36_LACLM 1 116 DBREF 7QZ6 B 1 116 UNP A2RI36 A2RI36_LACLM 1 116 SEQADV 7QZ6 HIS A 117 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS A 118 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS A 119 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS A 120 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS A 121 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS A 122 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS B 117 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS B 118 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS B 119 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS B 120 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS B 121 UNP A2RI36 EXPRESSION TAG SEQADV 7QZ6 HIS B 122 UNP A2RI36 EXPRESSION TAG SEQRES 1 A 122 MET ALA GLU ILE PRO LYS GLU MET LEU ARG ALA GLN THR SEQRES 2 A 122 ASN VAL ILE LEU LEU ASN VAL LEU LYS GLN GLY ASP ASN SEQRES 3 A 122 TYR VAL TYR GLY ILE ILE LYS GLN VAL LYS GLU ALA SER SEQRES 4 A 122 ASN GLY GLU MET GLU LEU ASN GLU ALA THR LEU TYR THR SEQRES 5 A 122 ILE PHE LYS ARG LEU GLU LYS ASP GLY ILE ILE SER SER SEQRES 6 A 122 TYR FTR GLY ASP GLU SER GLN GLY GLY ARG ARG LYS TYR SEQRES 7 A 122 TYR ARG LEU THR GLU ILE GLY HIS GLU ASN MET ARG LEU SEQRES 8 A 122 ALA PHE GLU SER FTR SER ARG VAL ASP LYS ILE ILE GLU SEQRES 9 A 122 ASN LEU GLU ALA ASN LYS LYS SER GLU ALA ILE LYS HIS SEQRES 10 A 122 HIS HIS HIS HIS HIS SEQRES 1 B 122 MET ALA GLU ILE PRO LYS GLU MET LEU ARG ALA GLN THR SEQRES 2 B 122 ASN VAL ILE LEU LEU ASN VAL LEU LYS GLN GLY ASP ASN SEQRES 3 B 122 TYR VAL TYR GLY ILE ILE LYS GLN VAL LYS GLU ALA SER SEQRES 4 B 122 ASN GLY GLU MET GLU LEU ASN GLU ALA THR LEU TYR THR SEQRES 5 B 122 ILE PHE LYS ARG LEU GLU LYS ASP GLY ILE ILE SER SER SEQRES 6 B 122 TYR FTR GLY ASP GLU SER GLN GLY GLY ARG ARG LYS TYR SEQRES 7 B 122 TYR ARG LEU THR GLU ILE GLY HIS GLU ASN MET ARG LEU SEQRES 8 B 122 ALA PHE GLU SER FTR SER ARG VAL ASP LYS ILE ILE GLU SEQRES 9 B 122 ASN LEU GLU ALA ASN LYS LYS SER GLU ALA ILE LYS HIS SEQRES 10 B 122 HIS HIS HIS HIS HIS MODRES 7QZ6 FTR A 67 TRP MODIFIED RESIDUE MODRES 7QZ6 FTR A 96 TRP MODIFIED RESIDUE MODRES 7QZ6 FTR B 67 TRP MODIFIED RESIDUE MODRES 7QZ6 FTR B 96 TRP MODIFIED RESIDUE HET FTR A 67 24 HET FTR A 96 23 HET FTR B 67 24 HET FTR B 96 23 HET DM1 A 201 66 HETNAM FTR FLUOROTRYPTOPHANE HETNAM DM1 DAUNOMYCIN HETSYN DM1 DAUNORUBICIN FORMUL 1 FTR 4(C11 H11 F N2 O2) FORMUL 3 DM1 C27 H29 N O10 FORMUL 4 HOH *22(H2 O) HELIX 1 AA1 PRO A 5 GLY A 24 1 20 HELIX 2 AA2 TYR A 27 SER A 39 1 13 HELIX 3 AA3 ASN A 46 ASP A 60 1 15 HELIX 4 AA4 THR A 82 SER A 112 1 31 HELIX 5 AA5 LYS B 6 GLY B 24 1 19 HELIX 6 AA6 TYR B 27 SER B 39 1 13 HELIX 7 AA7 ASN B 46 ASP B 60 1 15 HELIX 8 AA8 THR B 82 SER B 112 1 31 SHEET 1 AA1 2 ILE A 63 FTR A 67 0 SHEET 2 AA1 2 LYS A 77 LEU A 81 -1 O TYR A 78 N TYR A 66 SHEET 1 AA2 2 ILE B 63 GLY B 68 0 SHEET 2 AA2 2 ARG B 76 LEU B 81 -1 O TYR B 78 N TYR B 66 LINK C TYR A 66 N FTR A 67 1555 1555 1.34 LINK C FTR A 67 N GLY A 68 1555 1555 1.33 LINK C SER A 95 N FTR A 96 1555 1555 1.33 LINK C FTR A 96 N SER A 97 1555 1555 1.33 LINK C TYR B 66 N FTR B 67 1555 1555 1.33 LINK C FTR B 67 N GLY B 68 1555 1555 1.33 LINK C SER B 95 N FTR B 96 1555 1555 1.32 LINK C FTR B 96 N SER B 97 1555 1555 1.33 CRYST1 103.157 35.382 67.787 90.00 97.31 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 0.009694 0.000000 0.001244 0.00000 SCALE2 0.000000 0.028263 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014873 0.00000