HEADER DNA BINDING PROTEIN 10-SEP-19 6ST7 TITLE CRYSTAL STRUCTURE OF DOMAIN SWAPPED TRP REPRESSOR V58I VARIANT WITH TITLE 2 BOUND L-TRP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRP OPERON REPRESSOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: THE ACTUAL SEQUENCE IS THAT FROM THE UNIPROT ENTRY COMPND 7 P0A881 BUT WITH V58I MUTATION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: TRPR, RTRY, B4393, JW4356; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: T7 EXPRESS KEYWDS HOSTAL, L-TRP BINDING, DOMAIN SWAPPING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SPRENGER,C.L.LAWSON,J.CAREY,F.DROUARD,C.VON WACHENFELDT,A.SCHULZ, AUTHOR 2 S.LINSE,L.LO LEGGIO REVDAT 4 24-JAN-24 6ST7 1 REMARK REVDAT 3 14-JUL-21 6ST7 1 COMPND SOURCE JRNL REMARK REVDAT 3 2 1 DBREF SEQADV SEQRES HELIX REVDAT 3 3 1 SITE ATOM REVDAT 2 07-OCT-20 6ST7 1 REMARK REVDAT 1 30-SEP-20 6ST7 0 JRNL AUTH J.SPRENGER,C.L.LAWSON,C.VON WACHENFELDT,L.LO LEGGIO,J.CAREY JRNL TITL CRYSTAL STRUCTURES OF VAL58ILE TRYPTOPHAN REPRESSOR IN A JRNL TITL 2 DOMAIN-SWAPPED ARRAY IN THE PRESENCE AND ABSENCE OF JRNL TITL 3 L-TRYPTOPHAN. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 77 215 2021 JRNL REFN ESSN 2053-230X JRNL PMID 34196612 JRNL DOI 10.1107/S2053230X21006142 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9866 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 493 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 43.4100 - 3.8900 1.00 2481 131 0.2271 0.2535 REMARK 3 2 3.8900 - 3.0900 1.00 2335 122 0.2781 0.3292 REMARK 3 3 3.0900 - 2.7000 1.00 2288 121 0.3325 0.3629 REMARK 3 4 2.7000 - 2.4500 1.00 2269 119 0.3603 0.4070 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) : 0.413 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.865 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 81.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 96.33 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 : 0.002 875 REMARK 3 ANGLE : 0.388 1181 REMARK 3 CHIRALITY : 0.032 132 REMARK 3 PLANARITY : 0.003 153 REMARK 3 DIHEDRAL : 28.138 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 44 ) REMARK 3 ORIGIN FOR THE GROUP (A): -44.4843 15.4402 -5.7437 REMARK 3 T TENSOR REMARK 3 T11: 0.8799 T22: 0.6729 REMARK 3 T33: 0.6837 T12: -0.0508 REMARK 3 T13: 0.1099 T23: -0.0363 REMARK 3 L TENSOR REMARK 3 L11: 4.2908 L22: 3.0499 REMARK 3 L33: 6.3946 L12: 1.3838 REMARK 3 L13: -1.0355 L23: 0.1251 REMARK 3 S TENSOR REMARK 3 S11: -0.6036 S12: -0.6381 S13: -0.6575 REMARK 3 S21: 0.6194 S22: -0.0901 S23: -0.3717 REMARK 3 S31: 1.2427 S32: -0.4770 S33: 0.6175 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 45 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.7801 44.9395 3.0442 REMARK 3 T TENSOR REMARK 3 T11: 1.2191 T22: 0.9660 REMARK 3 T33: 0.8840 T12: -0.1618 REMARK 3 T13: -0.2418 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 4.5489 L22: 3.4935 REMARK 3 L33: 4.9277 L12: 5.0473 REMARK 3 L13: 5.6914 L23: 5.7518 REMARK 3 S TENSOR REMARK 3 S11: -0.8532 S12: 0.1976 S13: 0.5873 REMARK 3 S21: -0.6360 S22: 0.2922 S23: 0.3807 REMARK 3 S31: -0.9658 S32: 0.4428 S33: 0.6580 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9954 66.2943 20.4439 REMARK 3 T TENSOR REMARK 3 T11: 0.9257 T22: 0.8836 REMARK 3 T33: 0.9453 T12: 0.0188 REMARK 3 T13: -0.3165 T23: -0.2473 REMARK 3 L TENSOR REMARK 3 L11: 4.0420 L22: 5.4631 REMARK 3 L33: 4.9502 L12: 1.0254 REMARK 3 L13: -2.2263 L23: -3.2810 REMARK 3 S TENSOR REMARK 3 S11: 0.6423 S12: -0.8115 S13: 0.5697 REMARK 3 S21: 1.4131 S22: -0.1657 S23: -0.8533 REMARK 3 S31: -0.7768 S32: 1.3358 S33: -0.3792 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 6ST7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292103852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 45.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.49 REMARK 200 R MERGE (I) : 0.06270 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20950 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: MOLREP REMARK 200 STARTING MODEL: 6ST6 REMARK 200 REMARK 200 REMARK: BI-PYRAMIDAL, HEXAGONAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA HEPES, 100 MM SODIUM REMARK 280 CHLORIDE, 27.5-35%(V/V) ISOPROPANOL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 38.18667 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 76.37333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.28000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 95.46667 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 19.09333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.18667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 76.37333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 95.46667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 57.28000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 19.09333 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: 3030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 -19.09333 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 318 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 GLY A -1 REMARK 465 PRO A 0 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MI7 RELATED DB: PDB REMARK 900 CONTAINS WT TRPR IN DOMAIN SWAPPED FORM WITHOUT LIGAND REMARK 900 RELATED ID: 1JHG RELATED DB: PDB REMARK 900 DIMER OF V58I L-TRP BOUND TRPR DBREF 6ST7 A 1 105 UNP P0A881 TRPR_ECOLI 1 105 SEQADV 6ST7 GLY A -1 UNP P0A881 EXPRESSION TAG SEQADV 6ST7 PRO A 0 UNP P0A881 EXPRESSION TAG SEQADV 6ST7 ILE A 58 UNP P0A881 VAL 58 ENGINEERED MUTATION SEQRES 1 A 107 GLY PRO MET ALA GLN GLN SER PRO TYR SER ALA ALA MET SEQRES 2 A 107 ALA GLU GLN ARG HIS GLN GLU TRP LEU ARG PHE VAL ASP SEQRES 3 A 107 LEU LEU LYS ASN ALA TYR GLN ASN ASP LEU HIS LEU PRO SEQRES 4 A 107 LEU LEU ASN LEU MET LEU THR PRO ASP GLU ARG GLU ALA SEQRES 5 A 107 LEU GLY THR ARG VAL ARG ILE ILE GLU GLU LEU LEU ARG SEQRES 6 A 107 GLY GLU MET SER GLN ARG GLU LEU LYS ASN GLU LEU GLY SEQRES 7 A 107 ALA GLY ILE ALA THR ILE THR ARG GLY SER ASN SER LEU SEQRES 8 A 107 LYS ALA ALA PRO VAL GLU LEU ARG GLN TRP LEU GLU GLU SEQRES 9 A 107 VAL LEU LEU HET TRP A 201 15 HET IPA A 202 4 HETNAM TRP TRYPTOPHAN HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 TRP C11 H12 N2 O2 FORMUL 3 IPA C3 H8 O FORMUL 4 HOH *20(H2 O) HELIX 1 AA1 SER A 5 ASN A 32 1 28 HELIX 2 AA2 LEU A 34 LEU A 43 1 10 HELIX 3 AA3 THR A 44 ALA A 92 1 49 HELIX 4 AA4 PRO A 93 VAL A 103 1 11 CRYST1 86.830 86.830 114.560 90.00 90.00 120.00 P 61 2 2 12 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 0.011517 0.006649 0.000000 0.00000 SCALE2 0.000000 0.013298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008729 0.00000