HEADER TRANSCRIPTION 18-MAR-25 9NT5 TITLE CRYSTAL STRUCTURE OF ECLACI TRANSCRIPTION FACTOR ANCESTOR 1 BOUND TO TITLE 2 GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACI TRANSCRIPTION FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANCESTRAL SEQUENCE RECONSTRUCTION, TRANSCRIPTION FACTOR, LACI, KEYWDS 2 GLYCEROL, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.L.GEORGELIN,R.L.FRKIC,L.TAN,J.KACZMARSKI,C.J.JACKSON REVDAT 1 18-JUN-25 9NT5 0 JRNL AUTH R.GEORGELIN,R.L.FRKIC,L.TAN,J.KACZMARSKI,C.J.JACKSON JRNL TITL CRYSTAL STRUCTURE OF ECLACI TRANSCRIPTION FACTOR ANCESTOR 1 JRNL TITL 2 BOUND TO GLYCEROL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.67 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 37010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1881 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 34.3100 - 3.9300 1.00 2816 157 0.1709 0.2007 REMARK 3 2 3.9200 - 3.1200 1.00 2745 158 0.1793 0.1968 REMARK 3 3 3.1200 - 2.7200 1.00 2729 136 0.1956 0.2267 REMARK 3 4 2.7200 - 2.4700 1.00 2708 131 0.1919 0.2027 REMARK 3 5 2.4700 - 2.3000 1.00 2717 131 0.1962 0.2191 REMARK 3 6 2.3000 - 2.1600 1.00 2668 153 0.1925 0.2008 REMARK 3 7 2.1600 - 2.0500 1.00 2722 128 0.1875 0.2077 REMARK 3 8 2.0500 - 1.9600 1.00 2692 135 0.1876 0.2268 REMARK 3 9 1.9600 - 1.8900 1.00 2684 138 0.2398 0.2997 REMARK 3 10 1.8900 - 1.8200 1.00 2673 165 0.2709 0.2845 REMARK 3 11 1.8200 - 1.7700 1.00 2676 125 0.2664 0.2771 REMARK 3 12 1.7700 - 1.7200 1.00 2666 156 0.2758 0.3119 REMARK 3 13 1.7200 - 1.6700 1.00 2633 168 0.3309 0.3369 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.760 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 : 0.004 NULL REMARK 3 ANGLE : 0.719 NULL REMARK 3 CHIRALITY : 0.050 330 REMARK 3 PLANARITY : 0.008 403 REMARK 3 DIHEDRAL : 5.969 299 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 9NT5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1000294172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-20 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 45.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.60 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 21.00 REMARK 200 R MERGE FOR SHELL (I) : 5.03100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14.4% PEG 8000, 0.08 M SODIUM REMARK 280 CACODYLATE PH 6.2, 0.16 M CALCIUM ACETATE, 20 % GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.70867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.41733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.41733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 16.70867 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: 2900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -33.41733 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 609 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 627 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 58 REMARK 465 ARG A 59 REMARK 465 ARG A 60 REMARK 465 SER A 61 REMARK 465 LEU A 332 REMARK 465 TYR A 333 REMARK 465 PHE A 334 REMARK 465 GLN A 335 REMARK 465 GLY A 336 REMARK 465 LEU A 337 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 HIS A 127 -88.40 -114.60 REMARK 500 ASN A 128 -174.26 -174.48 REMARK 500 ALA A 133 46.67 -87.37 REMARK 500 GLN A 134 14.21 -143.20 REMARK 500 LEU A 147 51.45 -93.61 REMARK 500 PRO A 151 79.98 -114.79 REMARK 500 PRO A 211 -162.68 -71.35 REMARK 500 TRP A 218 -7.78 80.50 REMARK 500 PRO A 234 59.33 -69.56 REMARK 500 ASP A 235 52.59 -96.42 REMARK 500 ASP A 271 -42.42 131.88 REMARK 500 ARG A 323 -120.38 -122.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 9NT5 A 58 337 PDB 9NT5 9NT5 58 337 SEQRES 1 A 280 MET ARG ARG SER HIS THR ILE GLY VAL VAL THR THR GLY SEQRES 2 A 280 LEU SER PHE TYR GLY PRO SER GLN ILE LEU VAL GLY ILE SEQRES 3 A 280 GLU ARG ALA ALA ARG GLU HIS GLY TYR SER LEU LEU LEU SEQRES 4 A 280 ALA THR VAL HIS GLU ASP PRO ASP GLU VAL GLU GLU ALA SEQRES 5 A 280 ILE ASN THR LEU ARG GLU ARG ARG VAL ASP GLY ILE ILE SEQRES 6 A 280 ILE VAL ALA PRO HIS ASN SER GLU GLU GLU ALA GLN LEU SEQRES 7 A 280 ALA GLN GLU ALA GLY VAL PRO PRO VAL VAL PHE LEU SER SEQRES 8 A 280 ALA GLN PRO PRO GLY VAL PRO THR VAL SER VAL ASP GLN SEQRES 9 A 280 TYR ALA GLY ALA ARG LEU ALA THR GLU HIS LEU LEU ASP SEQRES 10 A 280 LEU GLY HIS ARG ARG ILE ALA LEU ILE THR GLY PRO GLN SEQRES 11 A 280 ASP TRP LEU GLU ALA ARG GLU ARG LEU GLN GLY TRP ARG SEQRES 12 A 280 GLU ALA LEU ALA GLU ALA GLY LEU PRO PRO PRO ALA VAL SEQRES 13 A 280 LEU GLN GLY ASP TRP SER ALA ALA SER GLY TYR GLU ALA SEQRES 14 A 280 ALA ARG GLN LEU LEU GLU GLN PRO ASP PHE THR ALA ILE SEQRES 15 A 280 PHE ALA ALA ASN ASP GLN MET ALA LEU GLY VAL LEU ARG SEQRES 16 A 280 ALA LEU HIS GLU ARG GLY LEU ARG VAL PRO ASP ASP VAL SEQRES 17 A 280 SER VAL VAL GLY PHE ASP ASP ILE PRO GLU SER ALA TYR SEQRES 18 A 280 PHE HIS PRO PRO LEU THR THR VAL ARG GLN ASP PHE GLU SEQRES 19 A 280 GLU LEU GLY ARG GLN ALA VAL GLU GLN LEU LEU GLU MET SEQRES 20 A 280 ILE GLU GLY GLU GLU PRO PRO PRO PRO ALA VAL LEU PRO SEQRES 21 A 280 PRO GLU LEU ILE VAL ARG GLU SER THR ALA PRO PRO GLU SEQRES 22 A 280 ASN LEU TYR PHE GLN GLY LEU HET GOL A 401 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *140(H2 O) HELIX 1 AA1 GLY A 75 HIS A 90 1 16 HELIX 2 AA2 ASP A 102 ARG A 116 1 15 HELIX 3 AA3 ASP A 160 LEU A 175 1 16 HELIX 4 AA4 TRP A 189 ALA A 206 1 18 HELIX 5 AA5 SER A 219 LEU A 231 1 13 HELIX 6 AA6 ASN A 243 ARG A 257 1 15 HELIX 7 AA7 ILE A 273 PHE A 279 5 7 HELIX 8 AA8 ASP A 289 GLU A 306 1 18 SHEET 1 AA1 4 SER A 93 VAL A 99 0 SHEET 2 AA1 4 THR A 63 THR A 69 1 N ILE A 64 O SER A 93 SHEET 3 AA1 4 VAL A 118 ILE A 123 1 O ASP A 119 N THR A 63 SHEET 4 AA1 4 VAL A 144 PHE A 146 1 O VAL A 145 N ILE A 123 SHEET 1 AA2 2 VAL A 157 VAL A 159 0 SHEET 2 AA2 2 ALA A 314 LEU A 316 1 O LEU A 316 N SER A 158 SHEET 1 AA3 4 VAL A 213 GLN A 215 0 SHEET 2 AA3 4 ILE A 180 THR A 184 1 N LEU A 182 O LEU A 214 SHEET 3 AA3 4 ALA A 238 ALA A 241 1 O PHE A 240 N ALA A 181 SHEET 4 AA3 4 SER A 266 VAL A 268 1 O VAL A 268 N ALA A 241 SHEET 1 AA4 2 THR A 285 ARG A 287 0 SHEET 2 AA4 2 GLU A 319 ILE A 321 -1 O ILE A 321 N THR A 285 CISPEP 1 VAL A 261 PRO A 262 0 6.45 CISPEP 2 HIS A 280 PRO A 281 0 -2.87 CRYST1 104.821 104.821 50.126 90.00 90.00 120.00 P 31 2 1 6 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 0.009540 0.005508 0.000000 0.00000 SCALE2 0.000000 0.011016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019950 0.00000 CONECT 2100 2101 2102 CONECT 2101 2100 CONECT 2102 2100 2103 2104 CONECT 2103 2102 CONECT 2104 2102 2105 CONECT 2105 2104 MASTER 271 0 1 8 12 0 0 6 2224 1 6 22 END