HEADER TRANSCRIPTION 07-JAN-22 7WJP TITLE STRUCTURE OF PADR-LIKE PROTEIN FROM LISTERIA MONOCYTOGENES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PADR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCRIPTIONAL REGULATOR,PADR FAMILY; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES; SOURCE 3 ORGANISM_TAXID: 1639; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LISTERIA MONOCYTOGENES, TRANSCRIPTION FACTOR, REGULATION, PADR, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.HONG,J.KIM REVDAT 2 29-NOV-23 7WJP 1 REMARK REVDAT 1 20-APR-22 7WJP 0 JRNL AUTH J.KIM,J.PARK,Z.CHOI,M.HONG JRNL TITL STRUCTURE-BASED MOLECULAR CHARACTERIZATION OF THE LLTR JRNL TITL 2 TRANSCRIPTION FACTOR FROM LISTERIA MONOCYTOGENES. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 600 142 2022 JRNL REFN ESSN 1090-2104 JRNL PMID 35219103 JRNL DOI 10.1016/J.BBRC.2022.02.067 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6224 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 318 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 36.0900 - 2.8300 1.00 3020 168 0.2135 0.2736 REMARK 3 2 2.8300 - 2.2500 1.00 2881 150 0.2737 0.3521 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) : 0.165 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.999 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.07 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 : 0.007 816 REMARK 3 ANGLE : 0.937 1099 REMARK 3 CHIRALITY : 0.046 123 REMARK 3 PLANARITY : 0.004 134 REMARK 3 DIHEDRAL : 19.609 492 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 22 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.1125 13.5384 9.7154 REMARK 3 T TENSOR REMARK 3 T11: 0.2550 T22: 0.4243 REMARK 3 T33: 0.6243 T12: 0.0558 REMARK 3 T13: -0.0452 T23: 0.1169 REMARK 3 L TENSOR REMARK 3 L11: 4.3268 L22: 3.2235 REMARK 3 L33: 7.4278 L12: 0.5816 REMARK 3 L13: -0.3505 L23: 2.7143 REMARK 3 S TENSOR REMARK 3 S11: -0.0763 S12: 0.2586 S13: -0.1742 REMARK 3 S21: -0.3189 S22: 0.1839 S23: 0.4184 REMARK 3 S31: -0.3544 S32: -1.0630 S33: -0.0102 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 23 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0272 21.8812 6.2894 REMARK 3 T TENSOR REMARK 3 T11: 0.3756 T22: 0.3634 REMARK 3 T33: 0.4606 T12: 0.0465 REMARK 3 T13: -0.0051 T23: 0.0589 REMARK 3 L TENSOR REMARK 3 L11: 3.5209 L22: 6.0361 REMARK 3 L33: 5.9150 L12: -0.1689 REMARK 3 L13: -0.3589 L23: 2.2168 REMARK 3 S TENSOR REMARK 3 S11: 0.2103 S12: 0.4204 S13: 0.4997 REMARK 3 S21: -0.5278 S22: -0.0841 S23: 0.1036 REMARK 3 S31: -0.5707 S32: -0.3187 S33: -0.1012 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 64 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9594 30.2106 5.9092 REMARK 3 T TENSOR REMARK 3 T11: 0.5674 T22: 0.4519 REMARK 3 T33: 1.0042 T12: -0.0056 REMARK 3 T13: 0.0167 T23: 0.1997 REMARK 3 L TENSOR REMARK 3 L11: 9.2363 L22: 9.4212 REMARK 3 L33: 8.4969 L12: 3.4346 REMARK 3 L13: -1.6601 L23: -2.1372 REMARK 3 S TENSOR REMARK 3 S11: -0.1292 S12: 1.7166 S13: 1.6498 REMARK 3 S21: -0.7412 S22: 0.8421 S23: -0.1298 REMARK 3 S31: -1.3323 S32: 0.0220 S33: -0.5810 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1476 5.3038 18.4443 REMARK 3 T TENSOR REMARK 3 T11: 0.5181 T22: 0.4148 REMARK 3 T33: 0.3213 T12: -0.0758 REMARK 3 T13: 0.0951 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 7.2876 L22: 3.7296 REMARK 3 L33: 2.3508 L12: 4.3924 REMARK 3 L13: 3.0308 L23: 1.1413 REMARK 3 S TENSOR REMARK 3 S11: 0.2742 S12: -0.7498 S13: -0.7070 REMARK 3 S21: 1.5571 S22: -0.3617 S23: -0.3628 REMARK 3 S31: 0.1000 S32: -0.4135 S33: 0.1272 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 7WJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6256 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : 0.38700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.250 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: 5ZQH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M LITHIUM CHLORIDE, 0.1 M MES, PH REMARK 280 6.5, 17% POLYETHYLENE GLYCOL 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 23.33500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.09100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.09100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.66750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.09100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.09100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.00250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.09100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.09100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.66750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.09100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.09100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.00250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.33500 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 23.33500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 203 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 212 LIES ON A SPECIAL POSITION. 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 GLU A 2 REMARK 465 VAL A 3 REMARK 465 ASN A 4 REMARK 465 ASN A 66 REMARK 465 GLU A 67 REMARK 465 GLY A 68 REMARK 465 GLU A 106 REMARK 465 ALA A 107 REMARK 465 VAL A 108 REMARK 465 ASN A 109 REMARK 465 GLU A 110 DBREF1 7WJP A 1 110 UNP A0A1D2INR9_LISMN DBREF2 7WJP A A0A1D2INR9 1 110 SEQRES 1 A 110 MET GLU VAL ASN PRO GLN PHE LYS LYS GLY VAL LEU GLU SEQRES 2 A 110 LEU CYS CYS LEU PHE LEU ILE GLN LYS LYS ASP CYS TYR SEQRES 3 A 110 GLY TYR GLU LEU ALA ASN GLN VAL SER LYS TYR ILE GLU SEQRES 4 A 110 VAL ALA GLU GLY ALA ILE TYR PRO VAL LEU ARG ARG LEU SEQRES 5 A 110 VAL LYS GLU GLU TYR CYS SER THR TYR LEU VAL GLU SER SEQRES 6 A 110 ASN GLU GLY PRO SER ARG LYS TYR TYR GLN LEU THR VAL SEQRES 7 A 110 LYS GLY GLU ILE TYR LEU ASN GLU LEU ILE SER GLU TRP SEQRES 8 A 110 ASN ASN PHE THR ASP SER VAL ALA LYS LEU LEU THR GLU SEQRES 9 A 110 GLY GLU ALA VAL ASN GLU FORMUL 2 HOH *17(H2 O) HELIX 1 AA1 GLN A 6 LYS A 23 1 18 HELIX 2 AA2 GLY A 27 SER A 35 1 9 HELIX 3 AA3 ALA A 44 GLU A 55 1 12 HELIX 4 AA4 THR A 77 THR A 103 1 27 SHEET 1 AA1 3 CYS A 25 TYR A 26 0 SHEET 2 AA1 3 ARG A 71 LEU A 76 -1 O TYR A 74 N CYS A 25 SHEET 3 AA1 3 CYS A 58 VAL A 63 -1 N TYR A 61 O TYR A 73 CRYST1 72.182 72.182 46.670 90.00 90.00 90.00 P 41 21 2 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 0.013854 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021427 0.00000